AMYB_SOYBN_svm.struc:
7777485: Sweet potato beta-amylase is a tetramer of identical subunits , which are arranged to exhibit 222 molecular symmetry .
7777485: Its subunit consists of 498 amino acid residues ( Mr 55,880 ) .
7777485: The crystals , growing to dimensions of 0.4 mm x 0.4 mm x 1.0 mm within 2 weeks , belong to the tetragonal space group P4(2)2(1)2 with unit cell dimensions of a = b = 129.63 A and c = 68.42 A. The asymmetric unit contains 1 subunit of beta-amylase , with a crystal volume per protein mass ( VM ) of 2.57 A3 / Da and a solvent content of 52 % by volume .
7777485: The refined subunit model contains 3,863 nonhydrogen protein atoms ( 488 amino acid residues ) and 319 water oxygen atoms .
7777485: The subunit structure of sweet potato beta-amylase ( crystallized in the absence of alpha-cyclodextrin ) is very similar to that of soybean beta-amylase ( complexed with alpha-cyclodextrin ) .
7777485: The root-mean-square ( RMS ) difference for 487 equivalent C alpha atoms of the two beta-amylases is 0.96 A. Each subunit of sweet potato beta-amylase is composed of a large ( alpha / beta)8 core domain , a small one made up of three long loops [ L3 ( residues 91 - 150 ) , L4 ( residues 183 - 258 ) , and L5 ( residues 300 - 327 ) ] , and a long C-terminal loop formed by residues 445 - 493 .
7777485: Conserved Glu 187 , believed to play an important role in catalysis , is located at the cleft between the ( alpha / beta)8 barrel core and a small domain made up of three long loops ( L3 , L4 , and L5 ) .
2430952: The blocked N-terminus and N-terminal sequence of soybean beta-amylase were determined by analyzing the acidic peptides derived on peptic digestion of the enzyme .
2430952: The acidic peptides were separated from the digest on a Dowex 50 X 2 column and purified by reversed phase-high performance liquid chromatography ( RP-HPLC ) .
2430952: The N-terminal 9 amino acid sequence of soybean beta-amylase was deduced to be acetyl-Ala-Thr-Ser-Asp-Ser-Asn-Met-(Gly-Leu ) from the results of sequence analysis of Pep-4 and amino acid analysis of other acidic peptides .
9918723: The final model included 500 amino acid residues , 141 water molecules and three glucose residues , which were located at subsites 1 - 2 and 4 in the active site .
9918723: The r.m.s. distance of 485 Calpha atoms between BBA-7s and SBA was 0.62 A. Out of the seven mutated amino acids , four ( Ser295Ala , Ile297Val , Ser351Pro and Ala376Ser ) were substitutions from the common residues with SBA to the thermostable forms .
9918723: A comparison of the structures of BBA-7s and SBA indicated that the side-chain of Ser376 makes new hydrogen bonds to the main-chain of an adjacent beta-strand , and that the side-chains of Val297 reduce an unfavorable interaction between the side-chains of Ala314 .
9918723: The mutation of Ser295Ala breaks the hydrogen bond between Ser295 OG and Tyr195 OH , which seems to be the reason for the unoccupied glucose residue at subsite 3 .
9918723: The tandem mutations at 350 - 352 including substitutions to two Pro residues suggested the reduction of main-chain entropy in the unfolded structure of this solvent-exposed protruded loop .
8103452: The complete amino acid sequence of a subunit of sweet potato beta-amylase , a homotetramer , was established by sequence analysis of peptides obtained by digestions with Achromobacter protease I and Staphylococcus aureus V8 protease and by cyanogen bromide cleavage of the S-carboxymethylated subunit .
8103452: The subunit of the enzyme is a single polypeptide consisting of 498 amino acid residues .
8103452: It showed 50 - 60 % identity in the amino acid sequence with those of beta-amylases from soybean and barley , while it about 25 % with those of three bacterial beta-amylases deduced from the cDNA sequences .
10617198: Here we report one of the first milestones of this project , the sequence of chromosome 4 .
10617198: Analysis of 17.38 megabases of unique sequence , representing about 17 % of the genome , reveals 3,744 protein coding genes , 81 transfer RNAs and numerous repeat elements .
10617198: Roughly 60 % of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes .
10617198: Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins .
9847126: The beta-amylase cDNA encoded a 55.95-kD polypeptide with a deduced amino acid sequence showing high similarity to other plant beta-amylases .
1837016: Unlike beta-amylases from other origins , the sweet potato beta-amylase is a tetramer of identical subunits , and it also bears starch phosphorylase-inhibitor activity .
1837016: A cDNA for the subunit of sweet potato beta-amylase was obtained by immunological screening of an expression cDNA library constructed by the vector-primer and linker method using a plasmid vector containing tac-SP6 promoters .
1837016: The SP6 transcript of a 2,000 base-pair-long cDNA insert directed the synthesis in vitro of a precursor to the subunit of beta-amylase which was identical in size with the mature subunit , and the beta-amylase mRNA detected by Northern blot hybridization was identical in size with the SP6 transcript of the cDNA insert .
1837016: The cDNA insert contained 1,494 base pairs of an open reading frame which codes for the 499-amino-acid-long precursor to the subunit of beta-amylase .
1837016: An amino acid sequence identical to the N-terminal amino acid sequence of the mature subunit appeared immediately after the initiator methionine of the precursor , indicating that the subunit of beta-amylase is synthesized as a mature form .
1837016: Comparison of the amino acid sequences of subunits of sweet potato beta-amylase and seed beta-amylases from barley and soybean indicated that these enzymes share about 68 % amino acid identities among each other .
1837016: Escherichia coli cells harboring the cDNA clone produced the mature-sized subunit of the beta-amylase , and the soluble extract exhibited amylolytic activity which migrated to the same position as the beta-amylase purified from the sweet potato in non-denaturing polyacrylamide gel containing soluble starch indicating that oligomerization of the subunit occurred properly in E. coli cells .
2446870: The mRNA is 1754 nucleotides long [ excluding the poly(A) tail ] and codes for a polypeptide of 535 amino acids with a relative molecular mass of 59,663 .
2446870: The deduced amino acid sequence was compared with the sequences of ten peptides obtained from the purified enzyme and unambiguous identification was obtained .
2446870: The N-terminal region of the deduced sequence was identical to a 12-residue cyanogen-bromide-peptide sequence , indicating that beta-amylase is synthesized as the mature protein .
2446870: A graphic matrix homology plot shows four glycine-rich repeats , each of 11 residues , preceding the C-terminus .
1383095: In the sequence of AmyB , the sequence that is identical to that of the cDNA was split into seven exons by six introns , and the transcription of this gene starts from multiple sites 26 to 30 bp downstream from a potential TATA-box sequence , 5'-TATATAA .
1383095: In the 5'-upstream region of AmyB , there are sequences homologous to those conserved in the 5'-upstream regions of genes encoding sporamin , which are regulated similarly to AmyB .
1383095: The 5'-upstream region of AmyB also contains sequences to which several previously known plant nuclear factors bind .
8334116: New crystallographic findings are presented which offer a deeper understanding of the structure and functioning of beta-amylase , the first known exo-type starch-hydrolyzing enzyme .
8334116: The model contains 491 amino acid residues , 319 water molecules , 1 sulfate ion , and 1 alpha-cyclodextrin molecule .
8334116: The protein consists of a core with an ( alpha / beta)8 supersecondary structure , plus a smaller globular region formed by long loops ( L3 , L4 , and L5 ) extending from beta-strands beta 3 , beta 4 , and beta 5 .
8334116: Between the two regions is a cleft that opens into a pocket whose floor contains the postulated catalytic center near the carboxyl group of Glu 186 .
8334116: Of the various alpha-cyclodextrin interactions with protein residues in loops L4 , L5 , L6 , and L7 , most notable is the shallow inclusion complex formed with Leu 383 ( in L7 , on the core side of the cleft ) through contacts of its methyl groups with the C-3 atoms of four of the ligand 's D-glucopyranosyl residues .
8334116: All six residues of the bound alpha-cyclodextrin are of 4C1 conformation and are joined by alpha-1,4 linkages with similar torsional angles to form a nearly symmetrical torus as reported for crystalline inclusion complexes with alpha-cyclodextrin .
8174545: To determine which amino acid residues are essential for the catalytic activity of soybean beta-amylase , deoxyoligonucleotide site-directed mutagenesis was employed against aspartyl , glutamyl , and cysteinyl residues located in highly conserved regions found in beta-amylase family to date .
8174545: Both substitution of aspartic acid at position 101 and that of glutamic acid at position 186 of the enzyme by neutral and acidic amino acids , respectively , led to the complete elimination of activity , but did not induce any significant changes in circular dichroic spectra or the binding affinity for cyclomaltohexaose , a substrate analogue .
8174545: Taking account of the results obtained here , the above two amino acid residues are involved in the catalytic site of soybean beta-amylase .
8174545: In contrast , substitution of cysteinyl residue at position 95 by a serinyl residue led to a drastic reducing of the optimal temperature ( from 50 degrees C to 30 degrees C ) , suggesting that this cysteinyl residue is responsible for the thermal stability of the enzyme .
9677422: The purified recombinant enzyme had properties nearly identical to those of native soybean beta-amylase and formed the same crystals as the native enzyme .
9677422: The cyclodextrins shared mainly two glucose binding sites , 3 and 4 .
9677422: The glucose residue 4 was slightly shifted from the maltose binding site .
9677422: This suggests that the binding site of the cyclodextrins is important for its holding of a cleaved substrate , which enables the multiple attack mechanism of beta-amylase .
8011643: Two molecules of beta-maltose substrate bind to the protein in tandem , with some maltotetraose enzymic condensation product sharing the same binding sites .
8011643: The beta-amylase soaked with maltal shows a similar arrangement of two bound molecules of 2-deoxymaltose , the enzymic hydration product .
8011643: In each case the nonreducing ends of the saccharide ligands are oriented toward the base of the protein 's active site pocket .
8011643: The catalytic center , located between the bound disaccharides and found deeper in the pocket than where the inhibitor alpha-cyclodextrin binds , is characterized by the presence of oppositely disposed carboxyl groups of two conserved glutamic acid residues .
8011643: Saccharide binding does not alter the spatial coordinates of these two carboxyl groups or the overall conformation of the 57-kDa protein .
8011643: However , the saccharide complexes of the active enzyme are associated with a significant ( 10 A ) local conformational change in a peptide segment of a loop ( L3 ) that borders the active site pocket.(ABSTRACT TRUNCATED AT 250 WORDS )
14593172: This approach resulted in completion of approximately 30 % of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome .
9046591: The cDNA encodes a predicted product of 488 amino acids with significant similarity to known beta-amylases from barley ( Hordeum vulgare ) , rye ( Secale cereale ) , and rice ( Oryza sativa ) .
9046591: Glycine-rich repeats found in the carboxyl terminus of the endosperm-specific beta-amylase of barley and rye are absent from the maize gene product .
9046591: The N-terminal sequence of the first 20 amino acids of a beta-amylase peptide derived from purified protein is identical to the 5th through 24th amino acids of the predicted cDNA product , indicating the absence of a conventional signal peptide in the maize protein .
8188635: The beta-amylase was deduced to be composed of 535 amino acid residues and its molecular weight was calculated to be 59,610 .
8188635: A comparison of the beta-amylase sequences from Haruna two-rows and Hiproly barleys revealed nine differences in the nucleotide sequence which resulted in three changes in the amino acid residues and 21 additional nucleotides at its 3'-end in the cultivar Haruna two-rows .
8188635: Lundgard and Svensson pointed out that 23 amino acid residues of the peptide fragment derived from the COOH-terminal region of barley ( cultivar Gula ) beta-amylase were in agreement with the deduced amino acid sequence reported by Kreis et al. , with the exception of a single position ( Met-527 compared to Ile ) [ Carlsberg Res .
8188635: In the cases of beta-amylases from soybean and sweet potato , the positions that corresponded to those at 233 and 347 in the amino acid sequence of beta-amylase from barley were Ala and Ser , respectively.(ABSTRACT TRUNCATED AT 250 WORDS )
9461215: Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases ( kb ) , and 54 % of the predicted genes had significant similarity to known genes .
8319688: The cDNA contained an open-reading frame composed of 496 amino acids .
8319688: The comparison of the amino acid sequence deduced from the cDNA with the N-terminal peptide sequence from mature enzyme proved that beta-amylase had no leader sequence .
8319688: His93 , involving an imidazole , and Asp348 , involving a carboxylate , in the highly conserved regions within the beta-amylases were replaced by Arg ( H93R ) and Ash ( D348N ) by site-directed mutagenesis , respectively .
8534999: In the sequence of the structural gene , a sequence identical to that of the cDNA was found to contain seven exons and six introns .
2474529: A radioactive peptide was finally isolated and its amino acid sequence was determined to be 181Leu-Gly-Pro-Ala-Gly-Glu186 .
1491009: Preliminary chain tracing showed that the enzyme folded into large and small domains .
1491009: The large domain has a ( beta alpha)8 super-secondary structure , while the smaller one is formed from two long loops extending from the beta 3 and beta 4 strands of the ( beta alpha)8 structure .
1491009: The interface of the two domains together with shorter loops from the ( beta alpha)8 structure form a deep cleft , in which alpha-cyclodextrin binds slightly away from the center .
1491009: One shares a binding site with alpha-cyclodextrin and the other is situated more deeply in the cleft .


ANXB_HUMAN_svm.struc:
7508441: The longest open reading frame encodes a 505-amino acid polypeptide , with a predicted molecular mass of 54.4 kDa .
7508441: cDNA sequencing revealed that the 56K cDNA shares a high degree of homology in both nucleotide ( 87 % ) and amino acid sequence ( 92.5 % ) with bovine annexin XI , indicating that the 56K cDNA encodes the human homologue of annexin XI , a member of the Ca(2+)-dependent phospholipid binding protein family .
7508441: Patients ' sera recognize preferentially the N-terminal region of the protein , which is specific for 56K / annexin XI and not shared by other annexins , indicating that the autoimmune response to 56K / annexin XI in these patients is specific for this annexin family member .
11013079: Exons 6 - 15 of the tetrad core repeat region differ from annexins A7 and A13 but are spliced identically to other phylogenetic descendents , making annexin A11 the putative primary progenitor of up to nine paralogous human annexins .
11013079: The 5 ' regions consist of untranslated exon 1 , followed by an extensive intron 1 comprising almost half the total gene length of > 40 kb , and additional GC-rich exons 2 - 5 encoding the proline - and glycine-rich amino-terminus .
1535225: Annexins are a family of structurally related calcium-dependent phospholipid binding proteins .
1535225: Two kinds of cDNAs were identified corresponding to annexin XI mRNA variants A and B , which are generated by alternative splicing of identical primary transcripts .
8938449: Mouse annexin XI ( anx11)2 was cloned from a macrophage cDNA library and characterized by genetic linkage mapping , DNA sequencing , and structural comparison with other annexins .
8938449: The open reading frame was flanked by long , untranslated regions and encoded a 503-amino-acid protein with 93.1 % identity to its human orthologue .
8938449: Its 189-aa amino terminus corresponded to the widely expressed variant 1 of two possible , alternatively spliced forms .
8938449: A previously described peptide from Aplysia brasiliana was identified as a closely related invertebrate homologue .
8938449: Since annexin XI is known to be localized in the nucleus at certain stages of development , the identification of a region in tetrad repeats 3 and 4 resembling the " chromo box" domain may be relevant to a nuclear regulatory function of annexin XI .
1380798: Sequence analysis of two overlapping clones revealed a 81-nucleotides 5'-nontranslated region , 1512-nucleotides of open reading frame , a 672-nucleotides 3'-nontranslated region , and a poly(A) tail .
1380798: Authenticity of the clones was confirmed by comparison of portions of the deduced amino acid sequence with eight sequences of proteolytic peptides obtained from rabbit lung protein .
1380798: CAP-50 cDNA encodes a 503 residue protein with a calculated M(r) of 54,043 and shows that the protein is composed of four imperfect repeats and hydrophobic N-terminal region .
1380798: C-terminal region including four imperfect repeats shows 58.1 % identity with human synexin ( annexin VII ) , 48.0 % identity with annexin I , 47.4 % identity with annexin II , 60.1 % identity with annexin IV , 54.5 % identity with annexin V .
1380798: Hydrophobic N-terminal region composed of 202 amino acid residues is not homologous with other annexin proteins suggesting that CAP-50 is a novel member of annexin family proteins .
1372001: Each protein consists of a conserved core domain having four ( or eight ) repeats of a segment approximately 70 amino acids in length and a nonconserved , usually short , amino-terminal domain .
1372001: To date , amino acid sequences for eight distinct mammalian annexins have been predicted from cDNAs .
1372001: The 503-amino acid deduced protein consists of a core domain of four annexin repeats and a long amino-terminal domain rich in glycine , proline , and tyrosine .


BRS3_HUMAN_svm.struc:
8131855: The deduced amino acid sequence shows about 86 % identity to that of guinea pig bombesin receptor .
9573346: Bombesin (BN)-like peptides / neurotransmitters mediate a broad range of physiological funtions in the gastrointestinal tract and the central nervous system through binding to their specific , high-affinity mammalian bombesin receptors .
9573346: The protein-coding region of both genes is divided into three exons and spans approximately 5kb .
8383682: Previously , two mammalian BN-like peptide receptor subtypes , gastrin-releasing peptide receptor and neuromedin-B receptor , have been cloned and characterized .
1325907: The cloned cDNA encodes a 399-amino-acid protein and shows the highest amino acid similarity to members of the bombesin receptor family ; 52 % and 47 % similarity to the gastrin-releasing-peptide ( GRP ) receptor and the neuromedin-B receptor , respectively .
10425452: The predicted amino acid sequence of ovine BRS-3 has approximately 85 % identity with the human , mouse and guinea pig receptors .
10425452: Highly conserved amino acids important in mediating receptor G-protein coupling to second messengers and important in ligand binding were found to be conserved in ovine BRS-3 .
10425452: One potentially important deviation was noted : ovine BRS-3 possesses an arginine residue at position 294 instead of a histidine residue as found in all other BRS-3 .


CB2R_HUMAN_svm.struc:
10688601: Sequence analysis of the coding region of the rat CB(2) genomic clone indicates 90 % nucleic acid identity ( 93 % amino acid identity ) between rat and mouse and 81 % nucleic acid identity ( 81 % amino acid identity ) between rat and human .
8679694: The 3.7 kb sequence contains an open reading frame encoding a protein of 347 residues sharing 82 % overall identity with the only other known peripheral receptor , human CB2 ( hCB2 ) and shorter than hCB2 by 13 amino acids at the carboxyl terminus .
8679694: Binding experiments with membranes from COS-3 cells transiently expressing mCB2 showed that the synthetic cannabinoid WIN 55212 - 2 had a 6-fold lower affinity for mCB2 than for hCB2 , whereas both receptors showed similar affinities for the agonists CP 55,940 , delta(9)-THC and anandamide and almost no affinity for the central receptor - ( CB1 ) specific antagonist SR 141716A .
9261404: In addition , proviral integrations were demonstrated within the 3 ' untranslated region of Cnr2 in five independent newly derived CasBrM-MuLV ( mouse murine leukemia virus ) tumors , CSL13 , CSL14 , CSL16 , CSL27 , and CSL97 .
12084572: The rat peripheral cannabinoid receptor ( rCB2 ) was cloned from a Sprague-Dawley rat spleen cDNA library and when translated , encodes a protein of 410 amino acids .
12084572: Alignment of rCB2 with mouse ( mCB2 ) and human ( hCB2 ) peripheral cannabinoid receptors reveals a high degree of homology except in the carboxy terminus where rCB2 is 50 and 63 residues longer than hCB2 and mCB2 , respectively .
12084572: PCR screening and sequencing of rat genomic DNA showed that rCB2 is encoded by three exons interrupted by two introns , one of which is polymorphic and contains a 209 base pair B2 ( SINE ) element .


DVL3_MOUSE_svm.struc:
8922524: The predicted amino acid sequence shares 64 and 62 % identity to Dvl1 and Dvl2 , respectively .
8922524: The region of highest conservation between all three Dvl coding regions , at 97 % identity , is noted at the PDZ domain ( also termed the DHR domain or GLGF motif ) , a motif of 60 amino acids present in all dishevelled encoded proteins and first described in the Drosophila discs large ( dlg ) tumor suppressor gene .
8817329: DVL-1 and DVL-3 putative protein products show 64 % amino acid identity .
8817329: The DVL-1 product is 50 % identical to dsh and 92 % to a murine dsh homologue ( Dvl-1 ) .
8644734: Sequences homologous to the 3 ' UTR of these transcripts ( DVL-22 ) were positioned within the DGS critical region and were found to be deleted in DGS patients .
9132266: Sequence analysis of the 5'-flanking region of the gene revealed a high GC content , six CCGCCC Sp-1-binding motifs , CREB , LBP-1 ( leader-binding protein 1 ) , and TGGCA-binding consensus sites .
7744250: A deletional analysis of Dsh identifies several conserved domains essential for activity , among which is a so-called GLGF / DHR motif .
8887313: dsh encodes the earliest-acting and most specific known component of the signal transduction pathway of Wingless , an extracellular signal homologous to Wnt1 in mice .
8887313: The Dvl2 amino acid sequence is equally related to the dsh sequence as is that of Dvl1 , but Dvl2 is most similar to the Xenopus homolog Xdsh .
8149913: The dishevelled gene encodes a novel intracellular protein that shares an amino acid motif with several other proteins that are found associated with cell junctions .
9192851: Amino acid similarity between the different Dishevelled proteins is concentrated in three highly conserved regions .
9192851: Two of these regions do not exhibit significant sequence similarity with other known proteins ; the third is similar to the discs-large homology region , which was first found in a Drosophila Discs-large tumor suppressor protein ( also known as GLGF or PDZ domain ) .
9298901: These results are consistent with an interpretation that common genetic mechanisms underlie abnormal social behavior and sensorimotor gating deficits and implicate Dvl1 in processes underlying complex behaviors .
8288125: dsh is expressed uniformly in the embryo and encodes a novel protein with no known catalytic motifs , although it shares a domain of homology with several junction-associated proteins .
8288125: Our results demonstrate that dsh encodes a specific component of Wg signaling and illustrate that Wnt proteins may utilize a novel mechanism of extracellular signal transduction .
9039502: In this series of projects of sequencing human cDNA clones which correspond to relatively long and nearly full-length transcripts , we newly determined the sequences of 80 clones , and predicted the coding sequences of the corresponding genes , named KIAA0201 to KIAA0280 .
9039502: The average size of the clones was 5.3 kb , and that of distinct ORFs in clones was 2.8 kb , corresponding to a protein of approximately 100 kDa .
9039502: Protein motifs that matched those in the PROSITE motif database were found in 25 genes and significant transmembrane domains were identified in 30 genes .
9039502: Taking into account of both the search data on sequence similarity and protein motifs , at least seven genes were considered to be related to transcriptional regulation and six genes to signal transduction .
9344861: The human DVL-3 gene encodes a predicted 716 amino acid protein which exhibits 98 % amino acid identity with mouse Dvl-3 and 49 % with Drosophila Dsh .
7958461: The 695-amino-acid protein encoded by the mouse dishevelled gene ( Dvl-1 ) shares 50 % identity ( 65 % similarity ) with dsh .
7958461: Similarity searches of protein and DNA data bases revealed that Dvl-1 encodes an otherwise novel polypeptide .
7958461: While no functional motifs were identified , one region of Dvl-1 was found to be similar to a domain of discs large-1 ( dlg ) , a Drosophila tumor suppressor gene .
7600981: Signaling factors of the Wnt proto-oncogene family are implicated in dorsal axis formation during vertebrate development , but the molecular mechanism of this process is not known .


ELIA_PHYCP_svm.struc:
7763784: We found that Phytophthora megasperma megasperma produces two elicitin isoforms , each belonging to a different physico-chemical class , although the beta elicitin was less toxic than other beta ones .
7763784: These 98 residue proteins were purified , sequenced and compared with other known elicitins .
7763784: In addition to the point mutation already known to correlate with the differences in necrotic activities between alpha and beta isoforms , we found another region of the molecule likely to be involved in the regulation of the toxicity .
2776750: They are proteins of similar Mr ( respectively 10,323 and 10,155 ) and their complete amino acid sequences were determined .
2776750: 85 % identity was observed between both sequences : only two short terminal regions are heterologous , while the central core is entirely conserved .
9385630: A set of 18 structures was calculated using 1360 NOE-derived distance restraints and 40 dihedral angle restraints obtained from 3JHNH alpha couplings .
9385630: The structure of beta cryptogein reveals a novel protein fold , with five helices and a double-stranded beta-sheet facing an omega-loop .
9385630: This cavity made of highly conserved residues represents a plausible binding site .
9385630: Residue 13 , which has been identified from directed mutagenesis and natural sequence comparison studies as a key amino acid involved in the differential control of necrosis , is surface exposed and could contribute to the binding to a ligand or a receptor .
9385630: The solution structure is close to the X-ray structure , with slight differences lightly due to the crystal packing .
1368359: The CD spectra showed that their secondary structure was largely conserved , exhibiting ca 50 % alpha-helix and little or no beta-structure .
1368359: These 98 residue proteins were sequenced and compared with other known elicitins .
8664508: Two of these genes encode distinct elicitins , and two genes would encode , if expressed , a class of highly acidic elicitins which had not been observed so far .
8125100: Difficulties encountered in the interpretation of two-dimensional NMR spectra of proteins exceeding roughly 100 amino acids , including resonance overlap and line broadening due to longer correlation times and / or aggregation phenomena , can be overcome by using three-dimensional 1H-NMR experiments .
8125100: Sequential assignment and secondary structure determination is illustrated for beta-sheet , alpha-helix and loop structures by analysis of planar cross sections perpendicular to the omega 2 or omega 3 axis at the amide proton resonance frequencies .
8125100: The secondary structure topology of the molecule is composed of five helices and an antiparallel beta-sheet .
8125100: Four of the helices compose two pairs running antiparallel while the last one is parallel to the beta-sheet .
8274771: Based on elicitin amino acid sequences , elicitin-coding sequences from P. parasitica were amplified by the polymerase chain reaction .
8274771: Elicitin was confirmed to be encoded as a precursor protein containing a 20-amino acid signal peptide that is processed before secretion .
8274771: Some isolates of P. parasitica that did not produce elicitins still contained elicitin-coding sequences but did not accumulate elicitin mRNA .
8031752: The backbone 1H and 15N resonance assignments and solution secondary structure determination of capsicein , a protein of 98 residues with a molecular mass of 10161 Da , are presented .
8031752: The sequential assignment was obtained for main - and side-chain resonances and led to the identification of all secondary structures .
8031752: This proved particularly useful for the assignment of degenerate amide protons of successive residues in alpha-helical structures .
8031752: The data show five alpha-helical regions comprising residues 5 - 18 , 26 - 33 , 44 - 58 , 59 - 67 , and 86 - 98 and a two-stranded antiparallel beta-sheet involving residues 70 - 75 and 80 - 85 , packed around a hydrophobic core grouping all of the aromatic residues .
8994969: BACKGROUND : Elicitins form a novel class of plant necrotic proteins which are secreted by Phytophthora and Pythium fungi , parasites of many economically important crops .
8994969: The overall structure has a novel fold consisting of six alpha helices and a beak-like motif , whose sequence is highly conserved within the family , composed of an antiparallel two-stranded beta sheet and an omega loop .
8994969: This motif is assumed to be a major recognition site for a putative receptor and / or ligand .
8994969: Two other distinct binding sites seem to be correlated to the level of necrotic activity of elicitins .
2583277: The phytopathogenic fungi Phytophthora cinnamomi cause systemic leaf necrosis on its non-host tobacco ; in culture , it secretes a protein , called cinnamomin , which elicits leaf necrosis and protects tobacco against the pathogen Phytophthora nicotianoe , in a way similar to cryptogein and different from capsicein , elicitins of known amino acid sequences .


FLGK_ECOLI_svm.struc:
11677609: The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria , sample sequencing of both S. enterica serovar Paratyphi A ( S. paratyphi A ) and Klebsiella pneumoniae , and hybridization of three unsequenced genomes to a microarray of S. typhimurium LT2 genes .
11677609: Most of these homologues were previously unknown , and 50 may be exported to the periplasm or outer membrane , rendering them accessible as therapeutic or vaccine targets .
2544561: We have determined the sequences of these genes and the flgJ gene and examined the deduced amino acid sequences of their products .
2544561: FlgH and FlgI , which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space , respectively , both had typical N-terminal cleaved signal-peptide sequences .
2544561: FlgH is predicted to have a considerable amount of beta-sheet structure , as has been noted for other outer membrane proteins .
2544561: FliF , as is usual for a cytoplasmic membrane protein of a procaryote , lacked a signal peptide ; it is predicted to have considerable alpha-helical structure , including an N-terminal sequence that is likely to be membrane-spanning .
2544561: The flgJ gene , immediately adjacent to flgI and the last gene of the flgB operon , encodes a flagellar protein of unknown function whose deduced sequence was hydrophilic and may correspond to a cytoplasmic protein .
2544561: A notable example occurs within the flgB operon , where between the end of flgG ( encoding the distal rod protein of the basal body ) and the start of flgH ( encoding the L-ring protein ) there was an unusually long noncoding region containing a potential stem-loop sequence , which could attenuate termination of transcription or stabilize part of the transcript against degradation .
2544561: Another example is the interface between the flgB and flgK operons , where transcription termination of the former may occur within the coding region of the latter .
8158647: The mutations mapped to the middle of flgL , to structural gene for HAP3 , and sequence analysis revealed the same coding change in both mutants : a substitution of cysteine for arginine 168 .
8158647: Our results show that the ability of a filament composed of normal flagellin subunits to resist mechanical stress depends on the structure of the protein ( HAP3 ) to which it is attached at its base .
8158647: The N-terminal sequence of HAP3 was found to be similar to the N-terminal sequence of flagellin , and the possibility that it provides a nucleation site for the C-terminal region of flagellin is discussed .
9278503: Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families ; many families of similar genes within E. coli are also evident .
9278503: The genome also contains insertion sequence ( IS ) elements , phage remnants , and many other patches of unusual composition indicating genome plasticity through horizontal transfer .
8905232: The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region from 12.7 to 28.0 minutes on the genetic map is described .
8905232: This region contains at least 681 potential open reading frames , of which 277 ( 41 % ) have been previously identified , 147 ( 22 % ) are homologous to other known genes , 139 ( 20 % ) are identical or similar to the hypothetical genes registered in databases , and the remaining 118 ( 17 % ) do not show a significant similarity to any other gene .
2193164: Within the bacterial flagellum the basal-body rod , the hook , the hook-associated proteins ( HAPs ) , and the helical filament constitute an axial substructure whose elements share structural features and a common export pathway .
2193164: We present here the amino acid sequences of the hook protein and the three HAPs of Salmonella typhimurium , as deduced from the DNA sequences of their structural genes ( flgE , flgK , flgL and fliD , respectively ) .
2193164: We compared these sequences with each other and with those for the filament protein ( flagellin ) and four rod proteins , which have been described previously ( Joys , 1985 ; Homma et al . ,
2193164: Hook protein most strongly resembled the distal rod protein ( FlgG ) and the proximal HAP ( HAP1 ) , which are thought to be attached to the proximal and distal ends of the hook , respectively ; the similarities were most pronounced near the N and C termini .
2193164: Hook protein and flagellin , which occupy virtually identical helical lattices , did not resemble each other strongly but showed some limited similarities near their termini .
2193164: HAP3 and HAP2 , which form the proximal and distal boundaries of the filament , showed few similarities to flagellin , each other , or the other axial proteins .
2193164: With the exceptions of the N-terminal region of HAP2 , and the C-terminal region of flagellin , proline residues were absent from the terminal regions of the axial proteins .
2193164: Moreover , with the exception of the N-terminal region of HAP2 , the terminal regions contained hydrophobic residues at intervals of seven residues .
2193164: In the case of the filament and the hook , the terminal regions are believed to be responsible for the quaternary interactions between subunits .
2193164: We suggest that this is likely to be true of the other axial structures as well , and specifically that interaction between N-terminal and C-terminal alpha-helices may be important in the formation of the axial structures of the flagellum .
2193164: Although consensus sequences were noted among some of the proteins , such as the rod , hook and HAP1 , no consensus extended to the entire set of axial proteins .
2181149: The hook protein ( FlgE ) , the most abundant protein in the complex , is present at approximately 130 subunits .
2181149: Hook-associated protein 1 ( FlgK ) is present at approximately 12 subunits .
2181149: The distal rod protein ( FlgG ) is present at approximately 26 subunits , while the proximal rod proteins ( FlgB , FlgC and FlgF ) are present at only approximately six subunits each .
2181149: Such values would correspond to either one or two turns of a helical structure with a basic helix of approximately 5.5 subunits per turn , which is the geometry of both the hook and the filament and , one supposes , the rod and hook-associated proteins .
2181149: These stoichiometries may derive from rules for the heterologous interactions that occur when a helical structure consists of successive segments constructed from different proteins ; the stoichiometries within the hook and the distal portion of the rod must , however , be set by different mechanisms .
2181149: The stoichiometries for the ring proteins are approximately 26 subunits each for the M-ring protein ( FliF ) , the P-ring protein ( FlgI ) , and the L-ring protein ( FlgH ) ; the protein responsible for the S-ring feature is not known .
2181149: The ring stoichiometries are discussed in light of other information concerning flagellar structure and function .
11677608: Notably , the genome sequence identifies over two hundred pseudogenes , several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium .


GAA6_CHICK_svm.struc:
11992121: We report that an Ala322Asp mutation in GABRA1 , encoding the alpha1 subunit of the gamma-aminobutyric acid receptor subtype A ( GABA(A)) , is found in affected individuals of a large French Canadian family with juvenile myoclonic epilepsy .
11992121: Compared with wildtype receptors , GABA(A) receptors that contain the mutant subunit show a lesser amplitude of GABA-activated currents in vitro , indicating that seizures may result from loss of function of this inhibitory ligand-gated channel .
1710013: We report the sequence of a complementary DNA ( cDNA ) that encodes the chicken GABAA receptor alpha 1 subunit , which is extremely homologous to mammalian alpha 1 subunits .
1710013: The distribution of alpha 1 subunit transcripts is shown to correlate mainly , but not completely , with the previously-reported pattern of benzodiazepine type I ( BZI ) binding sites in the avian brain .
1710013: These results suggest that the alpha 1 subunit may not necessarily be restricted to receptors having BZI pharmacology .
10602120: These are : Glutamate receptor subunit 3 ( GLUR3 ) , GABA receptor subunit alpha 3 ( GABRA3 ) , GABA receptor subunit e 1 ( GABRE1 ) , Vacuolar ATPase subunit 1 ( VATPS1 , XAP3 ) , the human homologue of plexin 3-SEX ( XAP6 ) and the Synaptobrevin-like protein ( SYBL1 ) .
1846404: gamma-Aminobutyric acidA ( GABAA ) receptors are multisubunit ligand-gated ion channels which mediate neuronal inhibition by GABA and are composed of at least four subunit types ( alpha , beta , gamma , and delta ) .
1846404: In cloning murine gamma 2-subunits , we isolated cDNAs encoding forms of the subunit that differ by the insertion of eight amino acids .
1846404: LLRMFSFK , in the major intracellular loop between proposed transmembrane domains M3 and M4 .
1846404: The two forms of the gamma 2-subunit are generated by alternative splicing , as demonstrated by cloning and partial sequencing of the corresponding gene .
2556293: Cloned cDNA encoding the bovine alpha 4 subunit of the GABAA receptor has been isolated .
2556293: The predicted 51 amino acid long mature protein contains an exceptionally long intracellular domain and shares 53 - 56 % sequence similarity to the previously characterized alpha 1 , alpha 2 and alpha 3 subunits .
2556293: Co-expression of alpha 4 and beta 1 in Xenopus oocytes resulted in the formation of GABA-gated chloride channels with expected pharmacology , although no benzodiazepine potentiation was observed .
3037384: Amino-acid sequences derived from complementary DNAs encoding the alpha - and beta-subunits of the GABA / benzodiazepine receptor from bovine brain show homology with other ligand-gated receptor subunits , suggesting that there is a super-family of ion-channel-containing receptors .
3037384: Co-expression of the in vitro-generated alpha-subunit and beta-subunit RNAs in Xenopus oocytes produces a functional receptor and ion channel with the pharmacological properties characteristic of the GABAA receptor .
9339354: A cDNA sequence of the gene coding for a 506 amino acid protein was identified , representing a member of a putative new class ( epsilon ) of the GABAA receptor .
9339354: The structure of the 5 ' region of most cDNAs is compatible with expression of protein sequence epsilon only in adult brain , whereas in other tissues , the majority of transcripts code for truncated protein sequences .
9339354: The GABRE gene extends over 14 kb and is clustered together with the alpha 3 and the putative beta 4 GABAA receptor subunit genes in an approximately 0.8-Mb interval in chromosome band Xq28 , located in the candidate regions of two different neurologic diseases .
9339354: Based on features of conservation of protein sequences , gene structure , and genomic organization of GABAA receptor gene clusters , we propose that the epsilon and gamma subunit genes have a common ancestor and that GABAA receptor gene clusters in the human genome have diverged by multiple duplication events of an ancestral gene cluster containing one each alpha , beta , and gamma / epsilon precursor gene .
2561977: Two cDNAs ( alpha 1 and alpha 4 ) from rat brain cDNA libraries encode isoforms of the alpha subunit of the GABA / benzodiazepine receptor , which differ at 30 % of their amino acid residues .
2561977: Northern blot analysis and in situ hybridization histochemistry show that alpha 1 and alpha 4 mRNAs have distinct sizes and distinct regional and cellular distributions in rat brain : both mRNAs are found in the cortex and hippocampus ; however , only the alpha 1 mRNA is detected in the cerebellum .
2561977: We injected RNA transcribed from alpha 1 and alpha 4 cDNAs into Xenopus oocytes , together with an RNA for a rat beta subunit .
2847710: A cDNA clone of an alpha subunit of the human GABA-A receptor has been isolated .
2847710: The human clone ( pCLL800 ) contains 1055 nucleotides in an open reading frame and 260 nucleotides in the 5 ' non-coding region .
2847710: The 351 amino acid sequence of this human alpha subunit shows 97 % homology with its bovine counterpart .
2847710: Developmental studies show that the levels of the rat alpha mRNA increase between one and three weeks of age in a manner similar to the development of the benzodiazepine binding sites .
1647983: We have utilized a polymerase chain reaction ( PCR ) strategy to identify a novel subunit , gamma 3 , of the GABAA receptor .
1647983: The gamma 3 cDNA encodes a mature protein of 450 amino acids that contains structural features typically conserved among subunits of the GABAA receptor family .
1647983: The gamma 3 subunit shares approximately 66 % sequence identity with the gamma 2 subunit but only 38 % and 29 % with alpha 1 and beta 1 subunits , respectively .
1647983: Localization of the gamma 3 mRNA indicates that it is widely distributed throughout the mouse brain in a pattern similar to that observed for mRNAs encoding the gamma 2 subunits .
1660002: When co-expressed with the alpha 5 - and beta 2-subunits in transfected cells a high potency for GABA ( Ka = 4.9 + / - 1.2 microM ) and a strong cooperativity in gating the channel ( H = 1.9 + / - 0.2 ) was observed .
1660002: An analogous bi-directional modulation of the GABA response was observed with diazepam and DMCM as tested with the subunit combinations alpha 1 beta 2 gamma 3 and alpha 3 beta 2 gamma 3 expressed in Xenopus oocytes .
8780005: The gamma-aminobutyric acid type A receptor cDNAs encoding the alpha 6 subunit homologues from chicken and goldfish have been cloned and sequenced .
8780005: Correspondingly , flunitrazepam-non-displaceable binding of [ 3H]Ro 15 - 4513 ( a benzodiazepine partial inverse agonist ) , which is a major characteristic of gamma-aminobutyric acid type-A receptors that contain the alpha 6 polypeptide , is also mainly found for cerebellar granule cells of fish and chick .
8780005: The conservation of this expression pattern suggests that gamma-aminobutyric acid type A receptors possessing the alpha 6 subunit are of fundamental importance for cerebellar function and that the corresponding gene regulatory elements , e.g. , granule cell-specific enhancers , have also been conserved .
2842688: When gamma-aminobutyric acid ( GABA ) , the major inhibitory neurotransmitter in vertebrate brain , binds to its receptor it activates a chloride channel .
2842688: We have now isolated cDNAs encoding two additional GABAA receptor alpha-subunits , confirming the heterogeneous nature of the receptor / chloride channel complex and demonstrating a molecular basis for it .
2842688: These alpha-subunits are differentially expressed within the CNS and produce , when expressed with the beta-subunit in Xenopus oocytes , receptor subtypes which can be distinguished by their apparent sensitivity to GABA .
2842688: Highly homologous receptor subtypes which differ functionally seem to be a common feature of brain receptors .
8632757: A cDNA encoding the human gamma-aminobutyric acidA ( GABAA ) receptor alpha 6 subunit has been cloned and sequenced .
8632757: The deduced amino acid sequence of this cDNA shows 91.4 % identity with the published rat alpha 6 subunit .
8632757: A number of compounds that bind to the benzodiazepine site potentiated the GABA response of alpha 6 beta 2 gamma 2 receptors .
1356407: Gamma-aminobutyric acid ( GABA ) , the major inhibitory neurotransmitter in brain , opens chloride channels through actions on GABAA receptors .
1356407: We now report base and amino acid sequences of the alpha 1 , alpha 2 , and alpha 3 subunits from GABAA receptors of audiogenic seizure-prone ( DBA / 2J ) and - resistant ( C57BL / 6J ) inbred strains of mice .
1356407: Inbreeding had fixed different alleles of the alpha 1 subunit in the two strains , giving five base differences in the cDNAs .
1356407: None of these affected amino acid sequence , but one did create a NsiI restriction site potentially useful in mapping genomic DNA .
1356407: No base or amino acid sequence differences between the strains were detected for the other two subunits .
1356407: Northern blots revealed no apparent strain differences in message levels for these three subunits in whole brains of the mice at 3 weeks of age , the peak of seizure susceptibility in DBA / 2J , but did reveal distinct regional and developmental patterns of expression among the subunits in mouse brain .
2166916: Benzodiazepines are widely prescribed anxiolytics and anticonvulsants which bind with high affinity to sites on the GABAA receptor / Cl - channel complex and potentiate the effect of the neurotransmitter GABA ( gamma-aminobutyric acid ) .
2166916: The heterogeneity of benzodiazepine recognition sites in the central nervous system was revealed by studies showing different classes of GABAA receptor subunits ( classes alpha , beta and gamma ) and variant subunits in these classes , particularly in the alpha-class .
2166916: Expression of recombinant subunits produces functional receptors ; when certain alpha-variants are coexpressed with beta - and gamma-subunits the resulting receptors have pharmacological properties characteristic of GABAA-benzodiazepine type I or type II receptors .
2166916: We show that recombinant receptors composed of alpha 6 , beta 2 and gamma 2 subunits bind with high affinity to the GABA agonist [ 3H]muscimol and the benzodiazepine [ 3H]Ro15-4513 but not the other benzodiazepines or beta-carboniles .
2166916: The same distinctive pharmacology is observed with GABAA receptors from rat cerebellum immunoprecipitated by an antiserum specific for the alpha 6 subunit .
8719414: A cDNA encoding the gamma 3 subunit of the human GABAA receptor has been obtained by molecular cloning .
8719414: Its deduced amino acid sequence shows a high level of sequence identity with the published mouse and rat sequences ( 96 % ) .
8719414: The ligand binding pharmacology of the benzodiazepine site formed by stably-expressed human alpha 5 beta 3 gamma 2S and alpha 5 beta 3 gamma 3 GABAA receptor subtypes have been compared for a number of ligands , Benzodiazepine site ligands were found to be either non-selective or gamma 2-selective , with the exception of CL218,872 , which was found to be 10-fold selective for the alpha 5 beta 3 gamma 3-containing subtype Two benzodiazepine site ligands .
8719414: Ro15-4513 and FG8205 were more efficacious at alpha 5 beta 3 gamma 3 receptors than alpha 5 beta 3 gamma 2 receptors expressed in Xenopus oocytes , CL218,872 , which is a partial agonist at alpha 1 containing receptors , had no intrinsic activity at either alpha 5 beta 3 gamma 2 or alpha 5 beta 3 gamma 3 , alpha 1 beta 2 gamma 2S and alpha 1 beta 2 gamma 3 human GABAA receptors were also expressed in Xenopus oocytes and their benzodiazepine pharmacology investigated .
8719414: Both the EC50 and efficacy of benzodiazepine site ligands were influenced by the type of gamma subunit coexpressed with alpha 1 and beta 2 .
9039914: Although there is widespread evidence that the sensitivity of GABA(A) receptors to anaesthetic agents is heterogeneous , the structural basis of these differences is largely unknown .
9039914: Variations in subunit composition can have profound effects on the sensitivity of GABA(A) receptors to modulatory agents such as benzodiazepines .
9039914: However , strict subunit specificity has not been demonstrated for the potentiating effects of anaesthetic agents .
9039914: Here we describe a new class of human GABA(A) receptor subunit ( epsilon ) that can assemble with alpha - and beta-subunits and confer an insensitivity to the potentiating effects of intravenous anaesthetic agents .
1849552: Its deduced amino acid sequence is 96 % identical to that of the alpha 2 polypeptide of the bovine GABAA receptor .
1849552: The polypeptide has features shared by all previously reported GABAA receptor alpha polypeptides and shares 71 - 76 % identity with previously described rat alpha polypeptides .
1849552: Most of the differences lie in the presumed extracellular and intracellular domains .
1849552: On Northern blots , the alpha 2 cDNA detects two mRNAs , which are found in cortex , hippocampus , and striatum , brain regions enriched in pharmacologically defined " BZ type II" receptors .
1849552: The distribution of alpha 2 mRNAs in rat brain suggests that the alpha 2 subunit may indeed be involved in the BZ type II receptors .
9527017: Gamma-aminobutyric acid (GABA)A receptors are the sites of action for many antiepileptic drugs such as benzodiazepines and barbiturates .
9527017: The mouse gamma1-subunit complementary DNA ( cDNA ) shares 98 % similarity with that of the rat at the level of amino acid sequence .
9527017: Northern blot hybridization indicates that the gamma1-subunit mRNA is expressed predominantly in areas other than the cerebral cortex and cerebellum and shows little change with postnatal development .
9527017: No differences have been found for the subunit between DBA / 2 and C57BL / 6 mice either for nucleotide sequence or for level of expression of the subunit 's mRNA in whole brain by Northern blots at 3 weeks of age .
9205108: A combination of cDNA library screening and 5 ' RACE analysis led to identification of three distinct mRNA isoforms of GABRA5 in human adult and fetal brain tissues , each of which differs only in the noncoding 5 ' UTR sequence .
9205108: Alignment of the genomic and cDNA sequences of GABRA5 revealed that the mRNA isoforms resulted from three alternative first exons 1A , 1B , and 1 C .
9205108: The GABRA5 promoter regions lacked TATA and CCAAT boxes but contained several other consensus transcriptional factor recognition sequences .
9084408: Conserved domains among members of previously described GABAA receptor subunits were used to design degenerate sense and antisense oligonucleotides .
9084408: The predicted protein has many of the features shared by other members of the ligand-gated ion channel family .
9084408: This channel subunit has significant amino acid identity ( 25 - 40 % ) with members of GABAA and GABAC receptor subunits and thus may represent a new subfamily of the GABA receptor channel .
8388764: In addition , a second gamma-aminobutyric acid ( GABAA ) receptor , the alpha 5 subunit , has been localized within the reference map to between GABRB3 and D15S12 .
1655526: A cDNA of rat brain encoding the GABAA receptor alpha 4 subunit has been cloned .
1655526: Recombinant receptors composed of alpha 4 , beta 2 and gamma 2 subunit bind with high affinity the GABA agonist [ 3H]muscimol and the benzodiazepine ' alcohol antagonist ' [ 3H]Ro 15 - 4513 , but fail to bind benzodiazepine agonists .
1655526: The alpha 4 subunit is expressed mainly in the thalamus , as assessed by in situ hybridization histochemistry , and may participate in a major population of thalamic GABAA receptors .
1311098: In coexpression experiments with the alpha 1 and beta 2 subunits , gamma 3 imparts benzodiazepine binding to gamma-aminobutyric acid type A receptors and forms gamma-aminobutyric acid-gated benzodiazepine-modulated chloride channels that exhibit a larger conductance than alpha 1 beta 2 receptor channels .
2538761: Neurotransmission effected by GABA ( gamma-aminobutyric acid ) is predominantly mediated by a gated chloride channel intrinsic to the GABAA receptor .
2538761: Co-expression of these subunits in heterologous systems generates receptors which display much of the pharmacology of their neural counterparts , including potentiation by barbiturates .
2538761: We now report the isolation of a cloned cDNA encoding a new GABAA receptor subunit , termed gamma 2 , which shares approximately 40 % sequence identity with alpha - and beta-subunits and whose messenger RNA is prominently localized in neuronal subpopulations throughout the CNS .
2538761: Importantly , coexpression of the gamma 2 subunit with alpha 1 and beta 1 subunits produces GABAA receptors displaying high-affinity binding for central benzodiazepine receptor ligands .
2167378: Since the isolation of cDNAs encoding GABAA receptor alpha 1 and beta 1 subunits , a further eight subunits have been identified .
2167378: These subunits show GABAA receptor heterogeneity , unpredicted from classical pharmacological studies .
2167378: I now report the isolation of a mouse cDNA clone encoding a novel GABAA receptor alpha subunit .
2167378: The striking feature of this subunit is its regional distribution in the mouse brain .
11003197: Candidate genes within this QTL encode the gamma-aminobutyric acid type A ( GABA A ) receptor gamma2 , alpha1 , alpha6 , and beta2 subunits .
11003197: We recently identified a coding sequence polymorphism between the B6 and D2 strains for the GABA A receptor gamma2 subunit gene ( Gabrg2 ) .
11326274: Generalized epilepsy with febrile seizures plus ( GEFS + ) , benign familial neonatal convulsions and nocturnal frontal lobe epilepsy , three autosomal dominant idiopathic epilepsies , result from mutations affecting voltage-gated sodium and potassium channels , and nicotinic acetylcholine receptors , respectively .
11326274: The K289M mutation affects a highly conserved residue located in the extracellular loop between transmembrane segments M2 and M3 .
2157817: A cDNA encoding a protein with 70 % amino acid identity to the previously characterized gamma-aminobutyric acidA ( GABAA ) receptor alpha-subunits was isolated from a rat brain cDNA library by homology screening .
2157817: As observed for alpha 1- , alpha 2- , and alpha 3-subunits , coexpression of this new alpha-subunit ( alpha 5 ) with a beta - and gamma 2-subunit in cultured cells produces receptors displaying high-affinity binding sites for both muscimol , a GABA agonist , and benzodiazepines .
2157817: Characteristic of GABAA / benzodiazepine type II sites , receptors containing alpha 2- , alpha 3 - or alpha 5-subunits have low affinities for several type I-selective compounds .
2157817: However , alpha 5-subunit-containing receptors have lower affinities for zolpidem ( 30-fold ) and Cl 218 872 ( three-fold ) than measured previously using recombinantly expressed type II receptors containing either alpha 2 - or alpha 3-subunits .
2165521: The structural requirements of fully functional GABAA receptors in the mammalian brain have remained elusive so far .
2165521: We report here on the cloning of the gamma 2-subunit cDNA of rat brain and its functional analysis by coexpression with the alpha 1 - and beta 1-subunits in Xenopus oocytes , and on the sites of gene expression of the 3 subunits in the rat brain .
2165521: In the absence of GABA , pentobarbital elicited a maximal current amplitude similar to that of GABA .
2165521: A minor population of channels is expressed which is open in the absence of GABA or pentobarbital .
1702226: Diversity of gamma-aminobutyrate type A ( GABAA ) receptors has recently been proposed to be achieved by assembly of receptor subtypes from a multitude of subunits ( alpha 1 - 6 , beta 1 - 3 , gamma 1 - 2 , and delta ) encoded by different genes .
1702226: Two forms of bovine gamma 2 subunit cDNA were isolated ( gamma 2S and gamma 2 L ) that differed by the presence or absence of a 24-base-pair ( 8-amino acid ) insertion in the cytoplasmic domain between the third and fourth putative membrane-spanning regions .
1702226: Polymerase chain reaction from RNA demonstrated that the two forms of gamma 2 subunit are expressed in bovine , human , and rat brain .
1702226: Sequencing of genomic DNA clones encoding the gamma 2 subunit demonstrated that the 24-base-pair insert is organized as a separate exon .
1702226: Analysis of the sequence of the 8-amino acid insert revealed that it contains a protein kinase C consensus phosphorylation site .
1702226: Expression of the large cytoplasmic loop domains of gamma 2S and gamma 2 L in Escherichia coli , followed by phosphorylation of the recombinant proteins by protein kinase C , demonstrated that gamma 2 L , but not gamma 2S , could be phosphorylated .
1702226: Thus the two forms of gamma 2 subunit differ by the presence or absence of a protein kinase C phosphorylation site .
9892355: Type-A receptors for the neurotransmitter GABA ( gamma-aminobutyric acid ) are ligand-gated chloride channels that mediate inhibitory neurotransmission .
9892355: Each subunit of the pentameric receptor protein has ligand-binding sites in the amino-terminal extracellular domain and four membrane-spanning regions , one of which forms a wall of the ion channel .
9892355: Each subunit also has a large intracellular loop that may be a target for protein kinases and be required for subcellular targeting and membrane clustering of the receptor , perhaps by anchoring the receptor to the cytoskeleton .
9892355: Other members of the superfamily of ligand-gated ion-channel receptors associate in postsynaptic-membrane clusters by binding to the proteins rapsyn or gephyrin .
9892355: Here we identify a new cellular protein , GABA(A)-receptor-associated protein ( GABARAP ) , which can interact with the gamma2 subunit of GABA(A) receptors .
9892355: GABARAP binds to GABA(A) receptors both in vitro and in vivo , and co-localizes with the punctate staining of GABA(A) receptors on cultured cortical neurons .
9892355: Sequence analysis shows similarity between GABARAP and light chain-3 of microtubule-associated proteins 1A and 1B .
2561970: Two cDNAs encoding novel GABAA receptor subunits were isolated from a rat brain library .
2561970: These subunits , gamma 2 and delta , share approximately 35 % sequence identity with alpha and beta subunits and form functional GABA-gated chloride channels when expressed alone in vitro .
2561970: The gamma 2 subunit is the rat homolog of the human gamma 2 subunit recently shown to be important for benzodiazepine pharmacology .
2561970: Cellular localization of the mRNAs encoding the gamma 2 and delta subunits in rat brain revealed that largely distinct neuronal subpopulations express the two subunits .
2561970: The delta subunit distribution resembles that of the high affinity GABAA receptor labeled with [ 3H]muscimol ; the gamma 2 subunit distribution resembles that of GABAA / benzodiazepine receptors labeled with [ 3H]flunitrazepam .
2561970: These findings have implications for the composition of two different GABAA receptor subtypes and for information processing in networks using GABA for signaling .
11326275: Epilepsies affect at least 2 % of the population at some time in life , and many forms have genetic determinants .
11326275: There is a recognized genetic relationship between FS and CAE , yet the two syndromes have different ages of onset , and the physiology of absences and convulsions is distinct .
8719416: Benzodiazepines modulate gamma-aminobutyric acid (GABA)-evoked chloride currents through a specific binding site at the GABAA receptor-chloride channel complex .
8719416: The heterogeneity of diazepam-sensitive benzodiazepine binding sites ( type I and type II ) has been identified by pharmacological approaches both with native receptors and recombinant receptors coexpressing alpha , beta and gamma subunits .
8719416: In addition , two distinguishable diazepam-insensitive benzodiazepine sites are found , spatially distributed between cerebral cortical and cerebellar regions .
8719416: Coexpression of alpha 6 with beta 2 and gamma 2 L subunits creates a pharmacologically similar benzodiazepine receptor to the diazepam-insensitive site observed in cerebellum , however , there is no evidence regarding the possible subunit combination forming the DI site in cerebral tissues .
8719416: Here we report the cloning of the human alpha 4 cDNA and its pharmacology by coexpression of this alpha 4 subunit with beta 2 and gamma 2 L subunits .
8719416: The pharmacology of the alpha 4 beta 2 gamma 2 L receptor complex appears to resemble those of the diazepam-insensitive site found in the cerebral cortex .
8719416: Our study thus suggests that this subpopulation of diazepam-insensitive GABAA receptors may be composed of alpha 4 beta 2 gamma 2 L subunits .
8391122: cDNAs encoding human alpha 2 and alpha 3 gamma-aminobutyric acidA receptor subunits have been cloned .
8391122: Their deduced amino acid sequences show much sequence identity with the published bovine sequences ( 98.2 % and 97.0 % for alpha 2 and alpha 3 , respectively ) .
8391122: Human alpha 1 beta 1 gamma 2 , alpha 2 beta 1 gamma 2 , alpha 3 beta 1 gamma 2 , and alpha 5 beta 1 gamma 2 subunit combinations were expressed in transiently transfected cells and their pharmacologies were characterized using a series of benzodiazepine ( BZ ) binding site ligands .
8391122: The partial inverse agonist Ro15-4513 showed an approximately 10-15-fold higher affinity for alpha 5-containing than for alpha 1- , alpha 2- , or alpha 3-containing receptors and is thus the first compound shown to have a significantly higher affinity for another receptor subtype than for alpha 1 beta 1 gamma 2 .
1848528: The murine GABAA / benzodiazepine ( GABAA / BZ ) receptor alpha 1 subunit cDNA has been isolated from a BALB / c mouse brain library and sequenced .
1848528: The cDNA is 2665 nucleotides long with an open reading frame of 455 amino acids .
1848528: It shows significant homology to the GABAA receptor alpha 1 subunit cDNA sequences of other species .
1848528: Excluding deletions , the murine GABAA alpha 1 receptor exhibits 96 % nucleotide and 100 % amino acid sequence homology to the rat alpha 1 receptor cDNA and over 91 % nucleotide and 98 % amino acid sequence homology to the bovine and human alpha 1 receptor cDNAs in the protein coding region .
2170110: The GABAA receptor gamma 1 subunit of human , rat and bovine origin was molecularly cloned and compared with the gamma 2 subunit in structure and function .
2170110: Both gamma subunit variants share 74 % sequence similarity and are prominently synthesized in often distinct areas of the central nervous system as documented by in situ hybridization .
2170110: When co-expressed with alpha and beta subunits in Xenopus oocytes and mammalian cells , the gamma variants mediate the potentiation of GABA evoked currents by benzodiazepines and help generate high-affinity binding sites for these drugs .
2170110: However , these sites show disparate pharmacological properties which , for receptors assembled from alpha 1 , beta 1 and gamma 1 subunits , are characterized by the conspicuous loss in affinity for neutral antagonists ( e.g. flumazenil ) and negative modulators ( e.g. DMCM ) .
2170110: These findings reveal a pronounced effect of gamma subunit variants on GABAA / benzodiazepine receptor pharmacology .
2153588: Two alpha subunits of the GABAA receptor in rat brain have been identified by molecular cloning .
2153588: The deduced polypeptide sequences share major characteristics with other chemically gated ion channel proteins .
2153588: One polypeptide represents the rat homologue of the alpha 3 subunit previously cloned from bovine brain , while the other polypeptide is a yet known subunit , termed alpha 5 .
2153588: When coexpressed with the beta 1 subunit in Xenopus oocytes the receptors containing the alpha 5 subunit revealed a higher sensitivity to GABA than receptors expressed from alpha 1 + beta 1 subunits or alpha 3 + beta 1 subunits ( Ka = 1 microM , 13 microM and 14 microM , respectively ) .
2153588: The alpha 5 subunit was expressed only in a few brain areas such as cerebral cortex , hippocampal formation and olfactory bulb granular layer as shown by in situ hybridization histochemistry .
2153588: Since the mRNA of the alpha 5 subunit was colocalized with the alpha 1 and alpha 3 subunits only in cerebral cortex and in the hippocampal formation the alpha 5 subunit may be part of distinct GABAA receptors in neuronal populations within the olfactory bulb .
8397108: We have isolated a cDNA , from the chicken , that encodes a fourth type of gamma subunit of the vertebrate brain GABAA receptor .
8397108: The mature polypeptide ( which we name gamma 4 ) displays 67 % , 69 % and 70 % identity , respectively , to the rat gamma 1 , gamma 2 and gamma 3 subunits .
2465923: The deduced amino acid sequences of cDNA clones encoding human GABAA receptor alpha 1 and beta 1 subunits are presented .
2465923: The human subunits display very high levels of sequence identity with the corresponding bovine receptor subunits .
2465923: The cloned human GABAA receptor subunits induce the formation of GABA-gated chloride channels when expressed in mammalian cells .
12466851: Of these transcriptional units , 4,258 are new protein-coding and 11,665 are new non-coding messages , indicating that non-coding RNA is a major component of the transcriptome .
12466851: 41 % of all transcriptional units showed evidence of alternative splicing .
12466851: In protein-coding transcripts , 79 % of splice variations altered the protein product .


HH1R_BOVIN_svm.struc:
8917588: From pharmacological studies using histamine antagonists and agonists , it has been demonstrated that histamine modulates many physiological functions of the hypothalamus , such as arousal state , locomotor activity , feeding , and drinking .
8917588: [ 3H]Doxepin has two saturable binding sites with higher and lower affinities in brains of wild-type mice , but H1R-deficient mice showed only the weak labeling of [ 3H]doxepin that corresponds to lower-affinity binding sites .
12142541: We report that congenic mapping links Bphs to the histamine H1 receptor gene ( Hrh1 / H1R ) and that H1R differs at three amino acid residues in VAASH-susceptible and - resistant mice .
8294913: It encodes a protein of 488 amino acids with a calculated molecular mass of 55,619 daltons compared with a size of 56 - 68 kDa for the photoaffinity-labeled receptor as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis .
8294913: Stable expression of the H1 receptor , characterized by the appearance of [ 3H]mepyramine binding sites with a pharmacology similar to that of the native H1 receptor , was obtained following transfection of Chinese hamster ovary cells .
8294913: Northern blot analysis of a variety of guinea pig peripheral or cerebral tissues identified , in most cases , a single transcript of 3.3 kb , but also , in some tissues , a second transcript of 3.7 kb , possibly generated by the use of different promoter or polyadenylation sites or corresponding to a transcript from a distinct gene .
8280179: The deduced protein of 487 amino acids showed characteristic properties of G-protein-coupled receptors .
8280179: Binding studies with [ 3H]pyrilamine on membranes from transfected cells revealed saturable specific binding with a KD of 1.2 nM and a Bmax of 3400 fmol / mg protein .
8280179: Binding affinities of histamine and known histamine antagonists were similar to those for histamine H1 receptors in guinea-pig cerebellum .
12595443: Furthermore , the genetic contribution of Bphs / Hrh1 to vasoactive amine sensitization is specific for histamine , since hypersensitivity to serotonin was unaffected by Bphs / Hrh1 .
7678492: The receptor protein deduced from this isolated gene was composed of 486 amino acids and showed characteristic properties of G protein-coupled receptors .
1722337: The H1 receptor cDNA encodes a protein of 491 amino acids ( Mr 55,954 ) with seven putative transmembrane domains , illustrating the similarity to other receptors that couple with guanine nucleotide-binding regulatory proteins ( G protein-coupled receptors ) .
1722337: The sequence homology between the H1 and H2 receptors is not higher than that between the histamine H1 and m1-muscarinic receptors .
8812432: The protein deduced from the nucleotide sequence is composed of 488 amino acid residues with characteristic properties of GTP binding protein-coupled receptors .
8282735: The gene contains no introns and encodes a protein of 488 amino acid residues .
8282735: The structure of the guinea-pig histamine H1 receptor is predicted to contain seven putative transmembrane regions , which are similar to those of receptors coupling with GTP binding proteins .
8282735: Although the third intracellular domain , the predicted binding site for the GTP binding protein , showed only 50 % identity with those of the bovine and rat H1 receptors , the expressed guinea-pig H1 receptor was fully able to bind with [ 3H]mepyramine .
8003029: The receptor protein deduced from the nucleotide sequence of this gene was composed of 487 amino acid residues with a calculated Mr of 55,781 and possessed characteristic properties of GTP binding protein-coupled receptors .
8003029: At the 5 ' flanking region of the human H1 receptor gene , we located potential TATA box and CACCC sequences , AP1 binding site-like sequences , glucocorticoid responsive element-like sequences , and other binding sequences for inducers .
12466851: Of these transcriptional units , 4,258 are new protein-coding and 11,665 are new non-coding messages , indicating that non-coding RNA is a major component of the transcriptome .
12466851: 41 % of all transcriptional units showed evidence of alternative splicing .
12466851: In protein-coding transcripts , 79 % of splice variations altered the protein product .


HUGA_VESVU_svm.struc:
8828537: Yellow jacket antigen 5 has been previously cloned and expressed in bacteria ; it contains 204 amino acid residues , and it has 69 % and 60 % sequence identities with the homologous proteins of white-faced hornet ( Dolichovespula maculata ) and wasp ( Polistes annularis ) , respectively .
8828537: These studies are now extended to yellow jacket hyaluronidase and phospholipase ; they contain 331 and 300 amino acid residues , respectively , and they show 92 % and 67 % sequence identity with their homologs of white-faced hornet .
7876212: The fragments were apparently generated by proteolysis of a Met-Met bond at residue 122 , as they were not observed for a Dol m 2 mutant with a Leu-Met bond .
7876212: Dol m 2 has 56 % sequence identity with the honey bee venom allergen hyaluronidase and 27 % identity with PH-20 , a human sperm protein with hyaluronidase activity .
7876212: A common feature of hornet venom allergens is their sequence identity with other proteins in our environment .
7876212: We showed previously the sequence identity of Dol m 5 with a plant protein and a mammalian testis protein and of Dol m 1 with mammalian lipases .
7682712: The venom of honeybees , Apis mellifera , contains several biologically active peptides and two enzymes , one of which is a hyaluronidase .
7682712: By using degenerate oligonucleotides derived from the amino-terminal sequence of this hyaluronidase reported by others , clones encoding the precursor for this enzyme could be isolated from a cDNA library prepared from venom glands of worker bees .
7682712: The deduced amino acid sequence showed that bee venom hyaluronidase is a polypeptide composed of 349 amino acids containing four cysteines and three potential sites for N-glycosylation .
7682712: The sequence of the precursor also indicated that the conversion of the pro-enzyme to the end product must involve cleavage of a Thr-Pro bond , a most unusual processing reaction .
10998264: The procedure , though applicable to N-glycosylated glycoproteins of any origin , is particularly devised for glycoproteins potentially containing fucose in alpha1,3-linkage to the reducing GlcNAc as may be found in plants and invertebrates , e.g. , insects and parasitic helminths .
10998264: Starting with an established procedure for mass spectrometric peptide mapping , the analysis of N-glycans by matrix-assisted laser desorption / ionization mass spectrometry involved the use of peptide : N-glycosidase A , a triphasic microcolumn for sample cleanup , and a new matrix mixture consisting of 2,5-dihyhydroxybenzoic acid , 1-hydroxyisoquinoline , and arabinosazone .
10998264: As an additional benefit , a peptide mass map is generated which serves to identify the analyzed protein .


KBF2_HUMAN_svm.struc:
9450761: Other mammalian Rel family members , including the proteins p52 , proto-oncoprotein c-Rel , and RelB , all have amino-terminal Rel-homology regions ( RHRs ) .
9450761: Here we report the crystal structure at 2.9 A resolution of the p50 / p65 heterodimer bound to the kappaB DNA of the intronic enhancer of the immunoglobulin light-chain gene .
9450761: This structure indicates why the p50 / p65 heterodimer interface is stronger than that of either homodimer .
9450761: A comparison of this structure with those of other Rel dimers reveals that both subunits adopt variable conformations in a DNA-sequence-dependent manner .
9865694: The presence of IkappaBalpha allows large en bloc movement of the NF-kappaB p65 subunit amino-terminal domain .
9865694: Amino acid residues immediately preceding the nuclear localization signals of both NF-kappaB p50 and p65 subunits are tethered to the IkappaBalpha amino-terminal ankyrin repeats , impeding NF-kappaB from nuclear import machinery recognition .
1339305: The deduced 607 amino acid sequence is identical to the sequence of the C-terminal region of 110 kd NF-kappa B protein .
1339305: A 70 kd protein can be identified in lymphoid cells using antibodies raised against the C-terminal region of p110 NF-kappa B .
1339305: Comparison of the two-dimensional tryptic peptide maps of the 70 kd protein expressed in cells and the in vitro translated product encoded by the cDNA display extensive homology .
1339305: The 70 kd protein expressed in bacteria prevents sequence-specific DNA binding of p50-p65 NF-kappa B heterodimer , p50 homodimer , and c-rel .
1339305: The 70 kd protein , predominantly found in lymphoid cells , is a new member of the I kappa B family of proteins and is referred to as I kappa B gamma .
9529257: The NFkappaB1 gene encodes two functionally distinct proteins termed p50 and p105 .
9529257: p50 corresponds to the N terminus of p105 and with p65 ( RelA ) forms the prototypical NF-kappaB transcription factor complex .
9529257: Our studies now demonstrate that p50 is generated by a unique cotranslational processing event involving the 26S proteasome , whereas cotranslational folding of sequences near the C terminus of p50 abrogates proteasome processing and leads to p105 production .
9950430: The transcription factor NF-kappaB is composed of homodimeric and heterodimeric complexes of Rel / NF-kappaB-family polypeptides , which include Rel-A , c-Rel , Rel-B , NF-kappaB / p50 and NF-kappaB2 / p52 .
9950430: Here we show that TPL-2 , which is homologous to MAP-kinase-kinase kinases in its catalytic domain , forms a complex with the carboxy terminus of p105 .
9950430: TPL-2 was originally identified , in a carboxy-terminal-deleted form , as an oncoprotein in rats and is more than 90 % identical to the human oncoprotein COT .
9950430: This releases associated Rel subunits or p50-Rel heterodimers to generate active nuclear NF-kappaB .
9865693: The structure of the IkappaBalpha ankyrin repeat domain , bound to a partially truncated NF-kappaB heterodimer ( p50 / p65 ) , has been determined by X-ray crystallography at 2.7 A resolution .
9865693: It shows a stack of six IkappaBalpha ankyrin repeats facing the C-terminal domains of the NF-kappaB Rel homology regions .
9865693: The first two repeats cover an alpha helically ordered segment containing the p65 nuclear localization signal .
9865693: The position of the sixth ankyrin repeat shows that full-length IkappaBalpha will occlude the NF-kappaB DNA-binding cleft .
1531086: The cDNA has an open reading frame of 900 amino acids capable of encoding a 97-kDa protein .
1531086: Like the 105-kDa precursor , it contains an amino-terminal Rel-related domain of about 300 amino acids and a carboxy-terminal domain containing six full cell cycle or ankyrin repeats .
1531086: In vitro-translated proteins , truncated downstream of the Rel domain and excluding the repeats , bind kappa B sites .
1531086: p50B is able to form heteromeric kappa B-binding complexes with RelB , as well as with p65 and p50 , the two subunits of NF-kappa B .
7510259: NF-kappa B is a transcription factor composed of the p50 and p65 subunits .
7510259: Recent works identified another human gene which encodes a molecule related to the p50 subunit , termed p50B , p49 or lyt-10 .
7510259: The deduced amino acid sequence of the precursor protein , p97 , shows conservation of the overall structure , and 86 % identity in the Rel homology domain ( RHD ) and 56 % identity in the ankyrin repeat domain ( ARD ) to human p50B / p97 .
1533881: We have isolated a chicken cDNA encoding p105 , the precursor protein for the p50 subunit of NF-kappa B .
1533881: Sequence analysis shows that chicken p105 is approximately 70 % identical to the mouse and human p105 proteins , containing the Rel homology domain in its N-terminal 370 amino acids and several ankyrinlike repeats in the C-terminal portion of the protein .
1533881: The Rel homology domain is particularly highly conserved between chicken and mammalian p50 , and an in vitro-synthesized , truncated chicken p105 protein , containing sequences that correspond to the predicted p50 protein , bound to a consensus kappa B site in an electrophoretic mobility shift assay .
1533881: In v-Rel-transformed chicken spleen cells , v-Rel is found in high-molecular-weight complexes which include cellular proteins of approximately 124 kDa ( p124 ) and 115 kDa ( p115 ) .
1992489: The DNA binding subunit of nuclear factor kappa B ( NF-kappa B ) , a B-cell protein that interacts with the immunoglobulin kappa light-chain gene enhancer , has been purified from nuclei of human HL-60 cells stimulated with tumor necrosis factor alpha ( TNF alpha ) , and internal peptide sequences were obtained .
1992489: The encoded open reading frame of about 105 kDa contained at its N-terminal half all six tryptic peptide sequences , suggesting that the 51-kDa NF-kappa B protein is processed from a 105-kDa precursor .
1992489: An in vitro synthesized protein containing most of the N-terminal half of the open reading frame bound specifically to an NF-kappa B binding site .
1992489: This region also showed high homology to a domain shared by the Drosophila dorsal gene and the avian and mammalian rel (proto)oncogene products .
1992489: Thus , both factors not only activate NF-kappa B protein , as described previously , but also induce expression of the gene encoding the DNA-binding subunit of NF-kappa B .
7969179: The NF-kappa B1 subunit of the transcription factor NF-kappa B is derived by proteolytic cleavage from the N terminus of a 105-kDa precursor protein .
7969179: The C terminus of p105NF-kappa B1 , like those of I kappa B proteins , contains ankyrin-related repeats that inhibit DNA binding and nuclear localization of the precursor and confer I kappa B-like properties upon p105NF-kappa B1 .
7969179: Here we report the characterization of two novel NF-kappa B1 precursor isoforms , p84NF-kappa B1 and p98NF-kappa B1 , that arise by alternate splicing within the C-terminal coding region of murine nfkb1 .
7969179: Transient transfection analysis revealed that p98NF-kappa B1 , but not p105NF-kappa B1 or p84NF-kappa B1 , acts as a transactivator of NF-kappa B-regulated gene expression and that this is dependent on sequences in the Rel homology domain required for DNA binding and on the novel 35 C-terminal aa of this isoform .
7969179: In contrast to previous findings , which indicated that p105NF-kappa B1 does not bind DNA , all of the NF-kappa B1 precursors were found to specifically bind with low affinity to a highly restricted set of NF-kappa B sites in vitro , thereby raising the possibility that certain of the NF-kappa B1 precursor isoforms may directly modulate gene expression .
9384558: Members of this family of proteins form homo - and heterodimers with differing affinities for dimerization .
9384558: They share a structural motif known as the rel homology region ( RHR ) , the C-terminal one third of which mediates protein dimerization .
9384558: These structures showed that the residues from the dimerization domains of both p50 and p65 participate in DNA binding and that the DNA-protein and protein dimerization surfaces form one continuous overlapping interface .
9384558: We desired to investigate the contribution of DNA to NFkappaB dimerization and to identify the mechanism for the selective association of rel / NFkappaB family peptides into transcriptionally active dimers .
9384558: RESULTS : We report here the crystal structures of the dimerization domains of murine p50 and p65 at 2.2 A and 2.0 A resolution , respectively .
9384558: A comparison of these two structures suggests that conservative amino acid changes at three positions are responsible for the differences in their dimer interfaces .
9384558: CONCLUSIONS : These two structures suggest that the rel / NFkappaB family of transcription factors use only a few conservative changes in their amino acid sequences to form a host of dimers with varying affinities for dimerization .
9384558: Amino acids at positions corresponding to 254 , 267 , and 307 of murine p50 , function as primary determinants for the observed differences in dimerization affinity .
9384558: The DNA-contacting charged amino acid sidechains from the dimerization domains are held in a similar conformation in both the DNA-bound and free states , therefore , no major structural rearrangement is required to bring these residues into contact with the DNA .
2203531: We have isolated a complementary cDNA coding for KBF1 and identified the DNA binding and dimerization domain of the protein .
2203531: Because KBF1 and the transcription factor NF-kappa B bind to similar sequences , we investigated the relationship between these two molecules .
2203531: It appeared that KBF1 is , by all criteria used , identical to the 50 kd DNA binding subunit of NF-kappa B .
2203531: KBF1 ( and therefore p50 ) also displays extensive amino acid sequence homology with the v-rel oncogene and the Drosophila maternal morphogen dorsal .
11094166: We found that RAC3 functions as a coactivator by binding to the active form of NF-kappa B and that overexpression of RAC3 restores GR-dependent transcription neglecting GR / NF-kappa B transrepression .
8036016: We have identified a rearrangement of the NFKB-2 gene in the HUT 78 human cutaneous T-cell leukemia ( CTCL ) line , cDNA and genomic DNA sequence predicted the presence of a truncated 80 kD NFKB-2 precursor protein ( p80HT ) , instead of the normal p100 protein .
7830764: The structure of a large fragment of the p50 subunit of the human transcription factor NF-kappa B , bound as a homodimer to DNA , reveals that the Rel-homology region has two beta-barrel domains that grip DNA in the major groove .
7830764: Both domains contact the DNA backbone .
7830764: The amino-terminal specificity domain contains a recognition loop that interacts with DNA bases ; the carboxy-terminal dimerization domain bears the site of I-kappa B interaction .
7830764: The folds of these domains are related to immunoglobulin-like modules .
7830764: The amino-terminal domain also resembles the core domain of p53 .
7969113: The genomic structure and sequence of NF-kappa B2 revealed the presence of two promoters and at least four kappa B regulatory elements , which mediate responsiveness to phorbol myristate acetate and tumor necrosis factor alpha .
7969113: We identified a nuclear complex which binds specifically to a subset of kappa B-related sites but not to the canonical kappa B element .
8230480: Full-length p100 only weakly binds DNA in vitro ; removal of the ankyrin-like repeats generates C-terminally truncated p100 proteins ( like p52 ) that have an increased ability to bind an oligonucleotide containing a kappa B site .
8230480: In addition , we show that chicken p100 is identical to a protein previously designated p115 , which is found in a complex with v-Rel in transformed chicken spleen cells .
9384586: The crystal structure of human NF-kappaB p52 in its specific complex with the natural kappaB DNA binding site MHC H-2 has been solved at 2.1 A resolution .
9384586: Whereas the overall structure resembles that of the NF-kappaB p50-DNA complex , pronounced differences are observed within the ' insert region ' .
9384586: This sequence segment differs in length between different Rel proteins .
9384586: Compared with NF-kappaB p50 , the compact alpha-helical insert region element is rotated away from the core of the N-terminal domain , opening up a mainly polar cleft .
9384586: The insert region presents potential interaction surfaces to other proteins .
9384586: Additional complexity in Rel protein-DNA interaction comes from an extended interfacial water cavity that connects residues at the edge of the dimer interface to the central DNA bases .
9384586: The observed water network might acount for differences in binding specificity between NF-kappaB p52 and NF-kappaB p50 homodimers .
8087845: The p105 precursor of the p50 subunit of NF-kappa B is processed in vitro by an ATP-dependent process that requires proteasomes and ubiquitin conjugation .
8087845: The C-terminal region of p105 is rapidly degraded , leaving the N-terminal p50 domain .
7530332: The 2.3-A crystal structure of the transcription factor NK-kappa B p50 homodimer bound to a palindromic kappa B site reveals that the Rel homology region folds into two distinct domains , similar to those in the immunoglobulin superfamily .
7530332: The p50 dimer envelopes an undistorted B-DNA helix , making specific contacts along the 10-base-pair kappa B recognition site mainly through loops connecting secondary structure elements in both domains .
7530332: The carboxy-terminal domains form a dimerization interface between beta-sheets using residues that are strongly conserved in the Rel family .
8398903: The p50 subunit of NF-kappa B is derived from the amino terminus of a 105 kilodalton precursor .
8398903: The p105 carboxyl terminus , which contains ankyrin-like repeats , a feature of I kappa B molecules , regulates the cytoplasmic retention of p105 and inhibits DNA binding by the precursor .
8398903: Here , we describe an I kappa B protein identical to the carboxyl-terminal region of p105 .
8398903: Probes spanning the COOH terminus but not the rel homology domain of p105 hybridize to a distinct 2.6-kilobase mRNA expressed in a wide range of murine tissues .
8398903: The nucleotide sequence of complementary DNA clones for this transcript , in vitro translation , and immune precipitation of metabolically labeled cell lysates establish that it encodes a 70 kilodalton protein that corresponds to the COOH-terminal 607 amino acids of p105 .
8398903: p70 phosphorylated by protein kinase A fails to inhibit DNA binding by p50 or the c-rel protein , and sequencing of radiolabeled p70 tryptic phosphopeptides establishes that protein kinase A phosphorylates serine residue 576 of p70 .
1876189: The transcription factor NF-kappa B is a protein complex which comprises a DNA-binding subunit and an associated transactivation protein ( of relative molecular masses 50,000 ( 50K ) and 65K , respectively ) .
1876189: Both the 50K and 65K subunits have similarity with the rel oncogene and the Drosophila maternal effect gene dorsal .
1876189: The 50K DNA-binding subunit was previously thought to be a unique protein , derived from the 105K gene product ( p105 ) .
1876189: We now report the isolation of a complementary DNA that encodes an alternative DNA-binding subunit of NF-kappa B .
1876189: It is synthesized as approximately 100K protein ( p100 ) that is expressed in different cell types , contains cell cycle motifs and , like p105 , must be processed to generate a 50K form .
1876189: A 49K product ( p49 ) can be generated independently from an alternatively spliced transcript ; it has specific kappa B DNA-binding activity and can form heterodimers with other rel proteins .
2203532: The DNA binding subunit of the transcription factor NF-kappa B , p50 , has been cloned .
2203532: Sequence analysis reveals remarkable homology for over 300 amino acids at the amino-terminal end to the oncogene v-rel , its cellular homolog c-rel , and the Drosophila maternal effect gene dorsal .
2203532: However , p65 appears homologous to c-rel , suggesting that c-rel may form heterodimers with p50 and rel may include a homodimerization motif .
11297557: The p105 precursor protein of NF-kappaB1 acts as an NF-kappaB inhibitory protein , retaining associated Rel subunits in the cytoplasm of unstimulated cells .
11297557: The p105 PEST domain contains a motif (Asp-Ser(927)-Gly-Val-Glu-Thr) , related to the IKK target sequence in IkappaBalpha , which is conserved between human , mouse , rat , and chicken p105 .
11297557: By using a specific anti-phosphopeptide antibody , it was confirmed that IKK2 overexpression induces serine 927 phosphorylation of co-transfected p105 and that endogenous p105 is also rapidly phosphorylated on this residue after TNFalpha or IL-1alpha stimulation .
11297557: Together these experiments indicate that the IKK complex regulates the signal-induced proteolysis of NF-kappaB1 p105 by direct phosphorylation of serine 927 in its PEST domain .


OTX2_BRARE_svm.struc:
7720578: The murine cognate , Otx2 , is first expressed in the entire epiblast of prestreak embryos and later in very anterior regions of late-gastrulae , including the neuroectoderm of presumptive fore - and mid-brain .
7720578: In particular , this homeodomain contains a specific lysine residue at position 9 of the recognition helix .
7720578: Microinjected transcripts of Xotx2 constructs containing a homeodomain where this lysine is substituted by a glutamine or a glutamic acid residue fail to cause these effects .
7898305: Three zebrafish otx homeoproteins containing a homeodomain homologous to that of the Drosophila orthodenticle head gap gene product have been identified by cloning and sequencing of cDNAs .
7898305: The zebrafish otx2 homeoprotein shares high amino-acid sequence identity with the mouse Otx2 homeoprotein , whereas the zebrafish otx1 and otx3 homeoproteins exhibit moderate homology with the mouse Otx1 and Otx2 homeoproteins .
7898305: The otx3 homeoprotein mRNA appears in the embryonic shield , the site of the organizer .
8613727: the regional pattern of expression of Otx1 , Otx2 , Dlx1 , Dlx2 , Dlx5 , and Emx1 is maintained in primary culture , suggesting that cells are already committed to a regional identity at this stage .
7893604: zOtx1 and zOtx2 encode predicted gene products which are 82 % and 94 % identical to the corresponding mouse proteins .
7893604: Between 9 and 14 h of development , zOtx transcripts disappear from forebrain regions in a manner characteristic for each gene , and from 14 to 24 h , particular regions of the forebrain and midbrain express one or both genes .
7893604: However , there are a number of interesting differences between the forebrain and midbrain regions which express the genes in the two species .
7931541: Within the cerebral and cerebellar cortices , neurons are organized in layers that segregate neurons with distinctive morphologies and axonal connections , and areas or regions that correspond to distinct functional domains .
7931541: Within the cerebellum , mRNAs for Otx1 and Otx2 are found within the external granular layer ( EGL ) , but in three spatially distinct domains .
1353865: Insight into the genetic control of the identity of specific regions along the body axis of vertebrates has resulted primarily from the study of vertebrate homologues of regulatory genes operating in the Drosophila trunk , but little is known about the development of most anterior regions of the body either in flies or vertebrates .
1353865: The Otx1 expression domain is similar to that of Otx2 , but contained within it .
1353865: The Emx2 expression domain is comprised of dorsal telencephalon and small diencephalic regions , both dorsally and ventrally .
1353865: Thus at the time when regional specification of major brain regions takes place , the expression domains of the four genes seem to be continuous regions contained within each other in the sequence Emx1 less than Emx2 less than Otx1 less than Otx2 .


PENK_XENLA_svm.struc:
1721992: Exon II contains the signal peptide and the N terminus of the mature protein .
1721992: Comparison to mammalian proenkephalin genomic sequence indicated that nucleotide sequences of the 5 ' flanking region , noncoding exon I and exon II were not well conserved but exon III was highly conserved .
7057924: The corresponding amino acid sequence shows that the precursor is 267 amino acids long and contains six interspersed Met-enkephalin sequences and one Leu-enkephalin sequence .
7057924: Five of the seven enkephalins are flanked on both sides by pairs of basic amino acid residues .
7057924: The precursors does not contain the sequences of the opioid peptides , dynorphin , alpha-neo-endorphin or beta-endorphin .
6547769: The structures of the genes coding for the opioid peptide precursors proopiomelanocortin , proenkephalin ( proenkephalin A ) and prodynorphin ( proenkephalin B ) , are known for some mammalian species .
6547769: The human proenkephalin gene consists of four exons , of which the main exon ( exon IV ) contains all known biologically active peptides--six Met-enkephalin sequences and one Leu-enkephalin sequence .
6547769: We report here the primary structures of the putative main exons of two proenkephalin genes in X. laevis , each of which codes for seven Met-enkephalin sequences but no Leu-enkephalin , indicating that Met-enkephalin preceded Leu-enkephalin in the evolution of the proenkephalin gene .
9126357: Mass spectrometry of fragments produced by limited proteolytic digestion of pro-enkephalin was used to locate the disulfide bridges in synenkephalin ( pro-enkephalin 1 - 73 ) , a domain which contains sorting information for targeting the pro-neuropeptide to the granules of the regulated secretory pathway in neuroendocrine cells .
9126357: Mass spectrometric analysis was optimized by using chemicals that gave low interference with the ionization and desorption processes , and computer software which simplified the identification of all possible disulfide-linked peptide fragments .
9126357: Protein conformational prediction of synenkephalin1-42 shows beta-turns which facilitate the formation of these disulfide bonds .


PRO2_HUMAN_svm.struc:
7758455: Potential structural differences of profilin I and profilin II that might explain the difference in actin binding are discussed .
7601111: Since functional characteristics for profilin II are lacking , we assayed the actin , the phosphatidylinositol 4,5-bisphosphate and the poly(L-proline) binding properties of this isoform .
7601111: This difference is explained by an amino acid exchange in the carboxy-terminal part of the protein which has been implicated in poly(L-proline) binding [ Björkegren , C. , Rozycki , M. , Schutt , C. , Lindberg , U. & Karlsson , R. ( 1993 ) FEBS Lett .
8365484: We have isolated a 1.7 kbp cDNA encoding a 140 amino acid protein ( 15.1 kDa , pI 5.91 ) with a high sequence similarity ( 62 % ) to human profilin ( profilin I ) .
11027290: It contains five exons that can generate four different transcripts by alternative splicing .
11027290: Two transcripts encode different profilin II isoforms ( designated IIa and IIb ) that have similar affinities for actin but different affinities for polyphosphoinositides and proline-rich sequences .
10600384: Like SH3 domains , profilin has a surface-exposed aromatic patch which binds to proline-rich peptides .
10600384: Humans express a basic ( I ) and an acidic ( II ) isoform of profilin which exhibit different affinities for peptides and proteins rich in proline residues .
10600384: Here , we report the crystallization and X-ray structure determination of human profilin II to 2.2 A. This structure reveals an aromatic extension of the previously defined poly-L-proline binding site for profilin I .
10600384: In contrast to serine 29 of profilin I , tyrosine 29 in profilin II is capable of forming an additional stacking interaction and a hydrogen bond with poly-L-proline which may account for the increased affinity of the second isoform for proline-rich peptides .
10600384: Differential isoform specificity for proline-rich proteins may be attributed to the differences in charged and hydrophobic residues in and proximal to the poly-L-proline binding site .
10600384: The actin-binding face remains nearly identical with the exception of five amino acid differences .
10600384: These observations are important for the understanding of the functional and structural differences between these two classes of profilin isoforms .
11034907: Here we describe the occurrence of two mouse profilin II isoforms , A and B , which are derived by alternative splicing .
11034907: They are identical through residue 107 of the protein , but then have distinct C-terminal sequences .
11034907: Profilin IIA binds to poly-L-proline and actin with high affinity similar to profilin I .


RBS_TOBAC_svm.struc:
3478552: We have cloned and sequenced all five members of the gene family for the small subunit ( rbcS ) of ribulose-1,5-bisphosphate carboxylase / oxygenase from tomato , Lycopersicon esculentum cv .
3478552: The Rbcs-2 gene contains three introns ; all the other members of the tomato gene family contain two introns .
3478552: The exon and intron sequences of Rbcs-3A are identical to those of Rbcs-3C , and differ by 1.9 % from those of Rbcs-3B .
3478552: Nucleotide sequence analysis suggests that the five rbcS genes encode four different precursors , and three different mature polypeptides .
3478552: S1 nuclease mapping of the 5 ' end of rbcS mRNAs revealed that the mRNA leader sequences vary in length from 8 to 75 nucleotides .
3557127: We have isolated and sequenced two cDNA clones ( LESS5 and LESS17 ) encoding the small subunit of ribulose-1,5-bisphosphate carboxylase of tomato ( Lycopersicon esculentum ) .
3557127: At the nucleotide level , the protein-coding regions of these genes are 85 % conserved , while the untranslated 3 ' regions are only 55 % conserved .
8299958: We determined the nucleotide sequences of five members of the rbcS gene family encoding the small subunit ( SSU ) of ribulose-1,5-bisphosphate carboxylase / oxygenase ( Rubisco ) of potato .
8299958: Within the two species , Lycopersicon esculentum and Solanum tuberosum , both members of the Solanaceae , the rbcS genes share more interspecific sequence identity , especially in the 5 ' - and 3'-untranslated regions and the intron sequences , than within one species .
8299958: However , the expression data of orthologous rbcS genes containing highly identical regulatory cis-acting elements were found to be different , suggesting that the simple finding of these motifs does not automatically imply similar transcriptional and / or post-transcriptional gene regulation .
8425051: DNase I footprinting assays were used to map sites of DNA-protein interaction in the promoter regions of three of the five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase ( rbcS ) in tomato .
8425051: These three genes share at least three DNA sequence motifs , including the G-box sequence , which are apparently not present in the other two tomato rbcS genes .
8425051: We find protection of one or more of these sequences in the aforementioned organs , indicating that the corresponding DNA-binding proteins could function in directing differential expression of the genes , although functional studies would be required to establish this point .
8425051: While most of the DNase I protections encompass previously identified conserved sequence motifs and their flanking sequence , we also observe protection of additional sequences , many of which occur in the region of the transcription start site .
4000958: We have cloned and sequenced a gene for the small subunit ( SS ) of ribulose bis-phosphate carboxylase-oxygenase from Nicotiana tabacum .
4000958: The tobacco gene is most closely related to the SS genes from the dicots soybean and pea , and less so to the monocots wheat and Lemna ; the deduced amino acid sequence of the mature protein is in all cases more closely conserved than is its chloroplast transit sequence .
4000958: Unlike the genomic sequences of the two monocots , which have one intron , and the two other dicots , which have two introns , the tobacco gene has three introns .
4000958: The third tobacco intron lies within a highly conserved region of the protein .
4000958: Its position coincides with the boundary of a 12 amino acid insertion in the SS genes of higher plants , relative to those of blue green algae .
4000958: The 5 ' flanking end of the gene carries 67 bp inverted repeats , which flank a series of eight direct repeats ; the direct repeats themselves each carry inverted repeats .
1512238: The structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase / oxygenase was refined at a resolution of 2.0 A to an R-factor of 17.1 % .
1512238: 1988 ) was extensively rebuilt , and the small subunit was retraced .
1512238: The refined model consists of residues 22 - 63 and 69 - 467 of the large subunit and the complete small subunit .
1512238: A striking feature of the model is that several loops have very high B-factors , probably representing mobile regions of the molecule .
1512238: An examination of the intersubunit contacts shows that the L8S8 hexadecamer is composed of four L2 dimers .
1512238: The dominant contacts between these L2 dimers are formed by the small subunits .
1512238: This suggests that the small subunits may be essential for maintaining the integrity of the L8S8 structure .
1512238: The active site shows differences between the unactivated form and the quaternary complex .
1512238: This residue lies on loop 6 of the alpha beta barrel , which is a particularly mobile loop .
1512238: The residues are held poised by a network of hydrogen bonds .
1512238: In the unactivated state , the active site is accessible to substrate binding .
3012537: The nuclear gene sequences encoding RBCS , the small subunit of ribulose-1,5-bisphosphate carboxylase / oxygenase ( EC 4.1.1.39 ) from several plants show extensive interspecific divergence but little intraspecific divergence , suggesting that these genes are evolving in concert within a genome .
3012537: In this study , the nucleotide sequences of two tomato ( Lycopersicon esculentum ) RBCS genes and a cDNA clone containing the entire coding region of a third tomato RBCS gene were determined .
3012537: Thus the tobacco gene seems to be phylogenetically as closely related to the tomato genes Rbcs-2A and Rbcs-3A as the latter two are to each other , and more closely related to them than Rbcs-1 is .
3012537: However , the mature part of the polypeptide encoded by the tobacco RBCS gene differs by five and six amino acids from the corresponding region in the polypeptides encoded by Rbcs-2A and Rbcs-3A , respectively , while these two tomato RBCS polypeptides differ from each other in the mature part by a single amino acid .
3012537: Rbcs-1 , whose nucleotide sequence shows higher divergence from both the tobacco RBCS gene and Rbcs-2A and Rbcs-3A , encodes a polypeptide whose mature part differs by eight amino acids from the corresponding region in the tobacco polypeptide but only by three and four amino acids from the corresponding regions of Rbcs-2A - and Rbcs-3A-encoded polypeptides , respectively .
3684569: Genomic clones containing three genes for the small subunit ( SSU ) of ribulose bisphosphate carboxylase were isolated from tobacco .
3684569: In addition , another clone was found to contain coding sequences which are 100 % homologous to a previously-cloned tobacco SSU gene ( Mazur , B.J. and Chiu , C-F .
6549380: The combination of cDNA and RNA sequencing techniques has enabled determination of the complete sequence of one of the mRNAs coding for the precursor of the small subunit of ribulose bisphosphate carboxylase of Nicotiana sylvestris .
6549380: In this 898-nucleotide-long mRNA , 540 nucleotides code for the entire 180-amino-acid-long precursor polypeptide consisting of the 57-amino acid-long transit peptide and the 123-amino-acid-long mature protein , while 60 and 195 nucleotides belong to the 5 ' and 3 ' noncoding flanking regions , respectively .
6549380: The 5 ' end , which is very rich in AG residues , contains several direct and indirect repeated sequences , and a possible hairpin structure .
6549380: The 3 ' end , terminated by a 103-nucleotide-long poly-A tail , is very rich in AU residues but does not contain the classical polyadenylation signal sequence .
3422467: One of these is a cDNA clone ; the other four are located on two genomic clones representing two different chromosomal loci containing one ( locus 1 ) and three genes ( locus 2 ) , respectively .
3422467: The intron / exon structure of the three genes in locus 2 is highly conserved with respect to size and position .
3422467: Although in most cases the amino acid sequences in the transit peptide part of different rbcS genes from the same species varied considerably more than the corresponding mature amino acid sequences , one exception found in tomato and potato indicates that the transit peptide of rbcS could have a special function .


SEP7_HUMAN_svm.struc:
9022087: GP Ib is composed of two subunits ( GP Ib(alpha) and GP Ib(beta)) each synthesized from separate genes .
9022087: This newly identified 5 ' gene contains an open reading frame encoding 369 amino acids with a high degree of sequence similarity to an expanding family of GTP-binding proteins .
8697812: Its transcript has an open reading frame of 1,218 nucleotides encoding 406 amino acids .
8697812: The deduced peptide sequence contained conserved domains rich in basic residues , GXXGXGKS--DXXG--TKXD , a motif of the GTPase superfamily .
9520435: Data analysis using cDNA / genomic DNA alignments and bio-informatic algorithms revealed 12 different predicted proteins , most of which are absent from bacterial databases , half of which are absent from Saccharomyces cerevisiae , and nearly all of which have relatives in Caenorhabditis elegans and Homo sapiens .
8152419: Their products are associated with the formation of a ring of neck filaments that forms at the region of the mother cell-bud junction during mitosis .
8152419: Not surprisingly , DNA sequence analysis reveals that the proteins share extensive homology at the amino acid level with their respective S. cerevisiae counterparts .
8152419: A database search revealed significant sequence similarity with two peptides , one from Drosophila and one from mouse , suggesting strong evolutionary conservation of function .
10591208: The genomic sequence provides access to the complete structures of all genes , including those without known function , their control elements , and , by inference , the proteins they encode , as well as all other biologically important sequences .
11859360: The centromeres are between 35 and 110 kilobases ( kb ) and contain related repeats including a highly conserved 1.8-kb element .
12747765: In addition , mRNA encoding tumor protein D52 was overexpressed in 60 % of breast cancer specimens , while transcripts encoding SNT-1 signal adaptor protein were downregulated in 70 % of these cases .
12537569: We compared the sequence of these clones to the annotated Release 3 genomic sequence , and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence .
12537569: This corresponds to at least one splice form for 40 % of the predicted D. melanogaster genes .
12537569: CONCLUSIONS : We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation .
12537569: Clones were eliminated either because they carry single nucleotide discrepancies , which most probably result from reverse transcriptase errors , or because they are truncated and contain only part of the protein-coding sequence .
9889007: We assigned two human expressed sequence tags ( ESTs ) , WI-15444 and SGC32067 , homologous to mouse brain protein h5 , to the critical region for Meckel syndrome ( MKS ) on 17q22-q23 .
8590280: The results of a computer search of public databases indicated that the sequences of 13 genes were unrelated to any reported genes , while the remaining 27 genes carried sequences which showed some similarities to known genes .
8590280: A stretch of triplet repeats was contained in each of three genes : These were GAG(Glu) in KIAA0122 and KIAA0147 , and TCC(Ser) in KIAA0150 .
8590280: A stretch of 10 amino acid-residues was repeated 21 times in KIAA0139 , and a homologous sequence of 76 - 78 nucleotides was found repeated 6 times in the untranslated region of KIAA0125 .
12537572: RESULTS : Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged , the revised annotation significantly improves gene models , resulting in structural changes to 85 % of the transcripts and 45 % of the predicted proteins .
12537572: Finally , cDNA sequence provided evidence for dicistronic transcripts , neighboring genes with overlapping UTRs on the same DNA sequence strand , alternatively spliced genes that encode distinct , non-overlapping peptides , and numerous nested genes .
9385360: The predicted protein has P-loop nucleotide binding and GTPase motifs .
8037772: We isolated a novel human cDNA , termed hCDC10 , whose predicted product showed a high degree of homology to the CDC10 protein of Saccharomyces cerevisiae .
8037772: This cDNA contained an open reading frame of 1254 nucleotides encoding 418 amino acids , which included a GTP-binding motif , GX4GKS--DX2G--KXD .
8037772: The predicted peptide sequence also revealed partial amino-acid identity ( 40 - 50 % ) with Diff 6 in Drosophila and with H5 in mouse .
8037772: Each of these sequence homologues , including Saccharomyces cerevisiae CDC10 , contains the GTP-binding motif .
11511094: Northern blot and in situ hybridization analysis showed that Bradeion has two distinct transcripts , approximately 2.2 and 1.7 kb length ( alpha and beta , respectively ) mainly in brain and slightly in heart , and no expression in any fetal organs .
11511094: The transcript of beta form lacks a hydrophobic region , which suggests that this form arises from a single Bradeion gene through unique RNA splicing .
2174398: The nucleotide sequence of this clone predicts a relatively hydrophilic protein characteristic of a cytoplasmic or nuclear protein .
12466851: Of these transcriptional units , 4,258 are new protein-coding and 11,665 are new non-coding messages , indicating that non-coding RNA is a major component of the transcriptome .
12466851: 41 % of all transcriptional units showed evidence of alternative splicing .
12466851: In protein-coding transcripts , 79 % of splice variations altered the protein product .
9611266: The HCDCREL-1 gene possesses a non-consensus polyadenylation signal that apparently is not efficiently utilized , resulting in the expression of a readthrough transcript also containing the platelet GPIb beta coding region .


STRP_STREQ_svm.struc:
8746458: This sequence coding for a 441 amino acid protein is well conserved among streptococcus species : there are two very conserved domains separated by a more variable region .
6760891: The protein consists of 415 amino acid residues .
6760891: The NH2-terminal 245 residues of streptokinase are homologous to the sequences of several serine proteases including bovine trypsin and Streptomyces griseus proteases A and B. The sequence alignment suggests that the active-site histidine-57 has changed to a glycine in streptokinase .
6760891: The other active-site residues , aspartyl-102 and serine-195 , are , however , present at the expected positions .
6760891: Streptokinase also contains internal sequence homology between the NH2-terminal 173 residues and a COOH-terminal 162-residue region between residues 254 and 415 .
6760891: Moderate homology in predicted secondary structures also exists between these two regions .
6760891: A COOH-terminal region of about 80 residues is apparently deleted from the second half of the duplicated structures .
6760891: These observations further suggest that the three-dimensional structure of streptokinase likely contains two independently folded domains , each homologous to serine proteases .
2989113: The protein is synthesized with a 26-amino acid residue N-terminal extension having properties characteristic of a signal peptide .
2989113: Comparison of the deduced amino acid sequence with the available amino acid sequence of a commercial streptokinase reveals minor primary structure differences .
2989113: Upstream from the skc gene , the putative skc promoter and the ribosome-binding site sequence have been identified ; downstream from the coding region , inverted repeat sequences thought to function as transcription terminators have been detected .
11296296: The complete or partial sequence of four different bacteriophage genomes is also present , with each containing genes for one or more previously undiscovered superantigen-like proteins .


TGR3_RAT_svm.struc:
1657407: The encoded receptor is an 853 amino acid protein with a large N-terminal extracellular domain containing at least one site for glycosaminoglycan addition , a single hydrophobic transmembrane domain , and a 41 amino acid cytoplasmic tail with no obvious signaling motif .
1657407: Introduction of the cDNA into COS cells and L6 myoblasts induces expression of a heterogenously glycosylated 280 - 330 kd protein characteristic of the type III receptor that binds TGF-beta 1 specifically .
7894484: We have identified mutations in three affected individuals : a C to G substitution converting a tyrosine to a termination codon , a 39 base pair deletion and a 2 basepair deletion which creates a premature termination codon .
8370410: Sequencing of the largest clone ( 3073 bp ) , revealed that the leader sequence contains 25 residues and that the 586 amino acids of the extracellular and transmembrane domains were identical to those described for endothelial endoglin .
8370410: However , the cytoplasmic tail encoded by this cDNA clone contains only 14 amino acids as opposed to the 47 residues previously reported , suggesting the existence of two alternative endoglin variants .
8370410: Both forms were shown to bind TGF-beta 1 and , when overexpressed in transfected mouse fibroblasts , to form disulfide-linked homodimers , indicating that the cysteine residues present in the extracellular domain are responsible for the dimerization .
8294451: The deduced sequence of the primary translated product of endoglin consists of 643 amino acids with a high sequence identity ( 96 % ) to human endoglin in the transmembrane and intracellular domains , but with a lower sequence similarity ( 66 % ) in the extracellular domain .
8294451: Antibodies , raised against a peptide corresponding to the intracellular domain of porcine endoglin , immunoprecipitated an 84-kDa protein under reducing condition and a 130-kDa protein under nonreducing condition in porcine aortic endothelial cells .
8294451: Endoglin was found to be coimmunoprecipitated with TGF-beta receptors type I and / or II by the endoglin antibodies or by TGF-beta receptor II antibodies in the presence of ligand .
8294451: Thus , endoglin and TGF-beta receptors I and / or II most likely formed a heteromeric receptor complex .
8294451: These results revealed that endoglin is a phosphorylated protein which forms a heteromeric complex with signaling receptors for TGF-beta .
10545596: Two types of mutant protein were previously analyzed , the product of an exon 3 skip which was expressed as a transient intracellular species and prematurely truncated proteins that were undetectable in patient samples .
10545596: Here we report the analysis of four proteins resulting from point mutations , with missense codons G52V and C53R in exon 2 , W149C in exon 4 and L221P in exon 5 .
10545596: Pulse-chase analysis with HUVECs from a newborn with the C53R substitution indicated that mutant endoglin remained intracellular as a precursor form and did not impair processing of the normal protein .
8125301: The mouse endoglin is a type-I integral membrane protein of 653 amino acids ( aa ) .
8125301: The human and mouse sequences display 71 % aa sequence identity with almost identical transmembrane and cytoplasmic domains .
8125301: Like its human counterpart , mouse endoglin displays significant sequence homology to the type-III TGF-beta receptor in two extracellular domains , as well as striking similarity in the transmembrane and cytoplasmic regions .
9245986: Five other mutations ( two donor splice-site mutations and three deletions ) produce altered mRNAs that are predicted to encode markedly truncated ENG proteins .
9245986: Mutations in other families are predicted to lie in ENG-regulatory regions or in one of the additional genes that may cause HHT .
9245986: Furthermore , because the clinical manifestation of disease in these eight families was similar , we hypothesize that phenotypic variation of HHT is not related to a particular ENG mutation .
10625079: Of the 16 mutations , 10 were novel , three had been independently identified in related families , and three were previously known .
1333192: The human TGF-beta type III receptor coding region encodes a protein of 849 amino acids with a single transmembrane domain and a short stretch of the intracellular domain .
1333192: Potential glycosaminoglycan attachment sites were found in the extracellular domain .
1333192: The overall amino acid sequence identities with those of the porcine and rat TGF-beta type III receptors were 83 % and 81 % , respectively .
1333192: A high degree of sequence conservation was observed in the transmembrane and intracellular domains , which also have sequence similarity with human endoglin .
1333192: In addition , two portions with 29 and 52 amino acids in the extracellular domain were found to be substantially similar with human endoglin .
1657406: As deduced from its cDNA sequence , the 853 amino acid core protein of betaglycan has an extracellular domain with clustered sites for potential attachment of glycosaminoglycan chains .
1657406: These chains are dispensable for TGF-beta binding to the core protein .
1657406: The transmembrane region and the short cytoplasmic tail of betaglycan are very similar to these regions in human endoglin , an endothelial cell membrane glycoprotein involved in intercellular recognition .
1657406: The ectodomain of betaglycan can be released as a soluble proteoglycan ; a potential cleavage site near the transmembrane region is identical to the highly regulated cleavage site of the membrane-anchored transforming growth factor-alpha precursor .
9157574: Using PCR-SSCP analysis followed by sequencing , we identified a C to A missense mutation in exon 4 which changed an Ala160 codon(GCT) to an Asp160 codon ( GAT ) .
8194490: We now report the cloning and sequencing of a full-length murine endoglin complementary DNA of 2902 base pairs which hybridizes specifically with a single messenger RNA ( mRNA ) species .
8194490: The transmembrane and cytoplasmic domains of all three proteins differ by two to four amino acids and are 70 % identical to the corresponding regions of the TGF beta binding protein , betaglycan .
8194490: After chemical cross-linking with [ 125I]TGF beta 1 and immunoprecipitation with the polyclonal antihuman endoglin serum , a radiolabeled band of mol wt 180,000 corresponding to dimeric endoglin was observed under nonreducing conditions , whereas a single band of mol wt 90,000 was seen under reducing conditions .
1692830: The N-terminal sequence of placental endoglin was determined and found within the deduced protein sequence , thus confirming the identity of the cDNA and revealing a partial signal peptide .
1692830: Endoglin is a type I integral membrane protein of Mr = 68,051 with an extracellular region of 561 amino acids , a hydrophobic transmembrane domain , and a 47-residue cytoplasmic tail .
1692830: There are four potential N-linked glycosylation sites in the N-terminal domain and a probable O-glycan domain rich in Ser and Thr residues proximal to the membrane-spanning domain .
1692830: The sequence contains an RGD tripeptide ( 374 - 376 ) , the first identified on a surface protein of endothelium .
9554745: Two identical missense mutations in unrelated families disrupt the start codon of the gene .
7864874: The deduced amino acid sequence of porcine ZP1 shared a 54 % and 63 % identity with those of mouse and human ZP2 , respectively .
7841460: Within the ZPA , ZPB and ZPC gene families , the DNA and deduced amino acid sequences are highly homologous to each other , and are most homologous between members of the same order within the class mammalia .
7841460: These results imply that all or most mammalian species express the ZPA , ZPB and ZPC proteins , which form the zona pellucida layer surrounding the oocyte .


VFUS_VACCC_svm.struc:
2795717: This showed that a 100 - to 115-kilobase ( kb ) centrally placed section is essentially colinear in organization in the two viruses and that a small region has translocated between the ends of one or other of the genomes during their divergence .
2795717: By using the cross-hybridization data , a 4-kb fragment of KS-1 DNA was identified , which corresponds to the regions of the cowpox virus and VV genomes containing genes for the orthopoxvirus A-type inclusion body protein ( " ATI" ) .
2795717: The sequence of the KS-1 DNA fragment contains homologs of genes which are on either side of the orthopoxvirus ATI genes but contains no homolog of the ATI gene itself .
2795717: Overall , these results show that the pattern of genomic conservation and variation between two poxvirus genera reflects the pattern within the orthopoxvirus genus but that , as observed previously , individual genes may not be present in genomic regions which are otherwise conserved in organization .
2219722: The genome consisted of 191,636 bp with a base composition of 66.6 % A + T. We have identified 198 " major" protein-coding regions and 65 overlapping " minor" regions , for a total of 263 potential genes .
2219722: Whereas several similarities to proteins of known function were discerned , the function of the majority of proteins encoded by these open reading frames is as yet undetermined .
2033392: The nucleotide sequence of a region of DNA 30 kb from the right end of the orf virus genome has been determined .
2033392: Examination of the sequences revealed an open reading frame encoding a 10K peptide with significant amino acid homology to the 14K ' fusion ' protein reported in vaccinia virus .
2033392: The orf virus sequence has a 31 % identity with the vaccinia virus protein , but a higher level of homology of core predicted residues .
2033392: The secondary structure of both proteins is also similar .
2033392: The occurrence of the TAAAT sequence upstream from the initiation codon indicates that the sequence is likely to be transcribed late in infection .
1856205: The gene rpo35 , encoding a subunit of the vaccinia virus DNA-dependent RNA polymerase , was identified , and its RNA and protein products were characterized .
1856205: Determination of the sequence of the DNA segment revealed four potential protein coding regions , none of which had evident similarity to any described RNA polymerase subunit of prokaryotes or eukaryotes .
1856205: One open reading frame that could encode a 35,400-Da protein was identified as rpo35 on the basis of mRNA hybridization , cell-free translation , and immunoprecipitation .
1856205: The identification was confirmed by sequencing tryptic peptides of the authentic Mr 35,000 RNA polymerase subunit .
2822962: There are two small hydrophobic regions , one at the C terminus ( 11 amino acids ) and the other at the N terminus ( 5 amino acids ) .
2822962: The protein contains two cysteines for oligomer formation and one glycosylation site .
2822962: Inspection of the deduced amino acid sequence of the 14-kilodalton protein revealed consensus sites with the hemagglutinin precursor of influenza A virus and with adenylate kinase and cytochrome c of various species .
2389560: We have identified the virus-induced fusion protein as a 14-kDa envelope protein , based on the ability of a 14-kDa specific monoclonal antibody ( mAbC3 ) to block vaccinia virus-induced fusion-from-within and fusion-from-without .
2389560: DNA sequence analyses of the 14-kDa encoding gene of the mutant viruses , 65 - 16 and 101 - 14 , reveal N-terminal deletions of 46 and 10 amino acids , respectively .
2389560: These deletions remove a small hydrophobic region at the N-terminus of the 14-kDa protein and prevent fusion .


VGLG_IHNV_svm.struc:
2741347: The deduced amino acid sequence of G shows that the encoded protein is a typical transmembrane glycoprotein of 524 amino acids containing a cleavable amino-terminal signal peptide , two potential N-linked glycosylation sites , a hydrophobic membrane anchor domain near the carboxy terminus , and a cytoplasmic domain at the carboxy terminus .
2741347: Somewhat unusual is the appearance of two charged amino acid residues , aspartate and arginine , within the putative membrane anchor sequence .
2741347: Like the viral G protein , the expressed G contained covalently linked palmitic acid .
2741347: However , unlike its vesicular stomatitis virus ( Indiana serotype ) counterpart , the Chandipura G protein has no potential palmitate-accepting cysteine residue within its cytoplasmic domain .
2741347: Thus , the covalent attachment of fatty acid to this molecule may occur at one or both of the cysteines within the membrane anchor domain .
1413521: The region contains two long open reading frames ( ORFs ) which are bounded by putative consensus ( AACAGG ) and polyadenylation ( CATG[A]7 ) sequences and are separated by an intergenic region of 53 nucleotides .
1413521: The first ORF encodes a polypeptide comprising 623 residues which was identified by peptide sequencing as the virion G protein .
1413521: The deduced amino acid sequence of the G protein includes putative signal and transmembrane domains and five potential glycosylation sites .
1413521: The second ORF encodes a polypeptide of 586 amino acids which also has characteristics of a rhabdovirus glycoprotein , including putative signal and transmembrane domains and eight potential glycosylation sites , and appears to correspond to a 90-kDa nonstructural glycoprotein ( GNS ) identified in BEFV-infected cells ( Walker et al .
1413521: A database search indicated that both the G and GNS proteins share significant amino acid sequence homology with other rhabdovirus G proteins and with each other .
3459163: Rabies cDNA clones , obtained by " walking along the genome" using two successive DNA primers , have allowed the sequence determination of the genes encoding the N , M1 , M2 , G , and the beginning of the L protein as well as the rabies intergenic regions .
3459163: Rabies intergenic regions are variable both in length and sequence .
6268840: The complete nucleotide sequences of the vesicular stomatitis virus mRNA 's encoding the glycoprotein ( G ) and the matrix protein ( M ) have been determined from cDNA clones that contain the complete coding sequences from each mRNA .
6268840: The G protein mRNA is 1,665 nucleotides long , excluding polyadenylic acid , and encodes a protein of 511 amino acids including a signal peptide of 16 amino acids .
6268840: G protein contains two large hydrophobic domains , one in the signal peptide and the other in the transmembrane segment near the COOH terminus .
6268840: Two sites of glycosylation are predicted at amino acid residues 178 and 335 .
6268840: The close correspondence of the positions of these sites with the reported timing of the addition of the two oligosaccharides during synthesis of G suggests that glycosylation occurs as soon as the appropriate asparagine residues traverse the membrane of the rough endoplasmic reticulum .
6268840: The mRNA encoding the vesicular stomatitis virus M protein is 831 nucleotides long , excluding polyadenylic acid , and encodes a protein of 229 amino acids .
6268840: The predicted M protein sequence does not contain any long hydrophobic or nonpolar domains that might promote membrane association .
6268840: The protein is rich in basic amino acids and contains a highly basic amino terminal domain .
6298453: The nucleotide sequence of the mRNA encoding the glycoprotein from the New Jersey serotype of vesicular stomatitis virus ( VSV ) was determined from a cDNA clone containing the entire coding region .
6298453: The mRNA is 1,573 nucleotides long ( excluding polyadenylic acid ) and encodes a protein of 517 amino acids .
6298453: Only six nucleotides occur between the translation termination codon and the polyadenylic acid .
6298453: An amino acid identity of 50.9 % was found for the two VSV serotypes .
6298453: Approximately 20 % identity was found between the rabies virus and VSV New Jersey glycoproteins .
6298453: The positions and sizes of the transmembrane domains , the signal sequences , and the glycosylation sites are identical in both VSV serotypes .
6298453: Two of five serine residues which were possible esterification sites for palmitate in the glycoprotein from the Indiana serotype are changed to glycine residues in the glycoprotein from the New Jersey serotype .
6298453: Because the glycoprotein of the New Jersey serotype does not contain esterified palmitate , we suggest that one or both of these residues are the probable esterification sites in the glycoprotein from the Indiana serotype .
2139267: The viral genome comprises 11,928 nucleotides and encodes the five viral proteins N , NS , M , G , and L. Deduced protein sequences are highly similar to those of the pathogenic PV strain , homologies ranging from 90.6 % for the M to 98.6 % for the L protein .
2139267: The strong conservation of both noncoding and coding nucleotide sequences indicates a high selective pressure on the primary structure of rabies virus genomic RNA .
1954257: The cDNA was 2035 bp long and contained two open reading frames ( ORF ) .
1954257: Although the protein encoded by this ORF displayed no similarity with other rhabdovirus proteins , it was supposed that the cDNA had been reverse-transcribed from a readthrough mRNA encoding successively for the M2 and the G proteins .
2822842: A cDNA copy of the entire coding region of the glycoprotein mRNA was cloned .
2822842: Nucleotide and deduced amino acid sequences were determined and compared to previously known sequences of other rhabdovirus glycoproteins to determine the relatedness of Sigma virus to other viruses of this group .
2985803: By recombining the cDNA clones in vitro and expressing the recombinants in COS cells , we were able to trace the critical lesion in tsO45 to a single substitution of a polar amino acid ( serine ) for a hydrophobic amino acid ( phenylalanine ) in a hydrophobic domain .
3033264: The nucleotide sequence of the mRNA encoding the glycoprotein of infectious hematopoietic necrosis virus was determined from a cDNA clone containing the entire coding region .
3033264: The G-protein cDNA is 1,609 nucleotides long ( excluding the polyadenylic acid ) and encodes a protein of 508 amino acids .
3033264: The predicted amino acid sequence was compared with that of the glycoprotein of the Indiana and New Jersey serotypes of vesicular stomatitis virus and with the glycoprotein of rabies virus , using a computer program which determined optimal alignment .
3033264: An amino acid identity of approximately 20 % was found between infectious hematopoietic necrosis virus and the two vesicular stomatitis virus serotypes and between infectious hematopoietic necrosis virus and rabies virus .
3033264: The positions and sizes of the signal sequence and transmembrane domain and the possible glycosylation sites were determined .
2168974: Phylogenetic analysis of the G gene sequences by maximum parsimony revealed four major lineages or subtypes within the classical VSV IND ( type 1 ) viruses , each with a distinct geographic distribution .
2168974: A high degree of VSV genetic diversity was found in Central America , with several virus subtypes of both VSV IND and NJ serotypes existing in this mainly enzootic disease region .
2168974: Nineteen percent sequence variation but no deletions or insertions were evident within the 5 ' noncoding and the coding regions of the VSV IND type 1 G genes .
2168974: In addition to numerous base substitutions , the 3 ' noncoding regions of these viruses also contained numerous base insertions and deletions .
2168974: As the VSV IND type 1 subtypes have diverged from the common ancestor with the NJ subtypes , their G mRNAs have accumulated more 3 ' noncoding sequence inserts , ranging up to 303 nucleotides in length .
2168974: Analysis of the deduced amino acid sequence differences among VSV IND type 1 viruses revealed numerous substitutions within defined antigenic epitopes , suggesting that immune selection may play a role in the evolution of these viruses .
1736537: A human strain isolated on cell culture from the saliva of a patient with clinical rabies had only five amino acid differences with the canine isolate , an indication of their close relatedness .
1736537: These differences could have originated during transmission from dog to dog , or from dog to man , or during isolation on cell culture ; they are nonetheless indicative of a genetic evolution of street rabies virus .
1736537: This evolution was further evidenced by the selection of cell-adapted variants which displayed new amino acid substitutions in the glycoprotein .
1736537: One of them concerned antigenic site III where arginine at position 333 was replaced by glutamine .
1736537: As expected this substitution conferred resistance to a site IIIa monoclonal antibody ( MAb ) , but surprisingly did not abolish neurovirulence for adult mice .
1736537: Two-thirds of the clones analyzed displayed from one to three amino acid substitutions .