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PR00986

Identifier
TRNASYNTHVAL  [View Relations]  [View Alignment]  
Accession
PR00986
No. of Motifs
5
Creation Date
17-SEP-1998  (UPDATE 07-JUN-1999)
Title
Valyl-tRNA synthetase signature
Database References
PRINTS; PR90000 TRNASYNTH; PR90001 TRNASYNTHCLI
PROSITE; PS00178 AA_TRNA_LIGASE_I
PFAM; PF00749 TRNA-SYNT_1
INTERPRO; IPR002303
Literature References
1. LODISH, H., BALTIMORE, D., BERK, A., ZIPURSKY, S.L., MATSUDAIRA, P.
AND DARNELL, J.
Nucleic Acids, the Genetic Code, and Protein Synthesis. 
IN MOLECULAR CELL BIOLOGY, SCIENTIFIC AMERICAN BOOKS (NEW YORK), 1995,
PP.126-128
 
2. DELARUE, M.
Aminoacyl-tRNA synthetases.
CURR.OPIN.STRUCT.BIOL. 5 48-55 (1995).
 
3. PERONA, J.J., ROULD, M. AND STEITZ, T.A.
Structural Basis for Transfer RNA Aminoacylation by Escherichia coli
Glutaminyl-tRNA Synthetase.
BIOCHEMISTRY 32 8758-8771 (1993).

Documentation
Appropriate attachment of an amino acid to its cognate tRNA is the key to
faithful translation of the genetic code. The family of enzymes responsible
for this is the aminoacyl-tRNA synthetases (AATRSs) (EC 6.1.1.-).
 
AATRSs catalyse a two-step reaction:
 
(1) Enzyme + amino acid + ATP ---> Enzyme(aminoacyl-AMP) + PPi
 
(2) tRNA + Enzyme(aminoacyl-AMP) ---> aminoacyl-tRNA + AMP + Enzyme
 
In the first step, they form an aminoacyl-adenylate, in which the carboxyl
of the amino acid is linked to the alpha-phosphate of ATP, by displacing
the pyrophosphate. When the correct tRNA is bound, the aminoacyl group is
transferred to the 2'- or 3'-terminal OH of the tRNA at the expense of AMP
[1].
 
Based on structural and sequence comparisons, this group of at least 20
proteins (in prokaryotes there are approximately 20, but in eukaryotes
there are usually 2 forms for each amino acid; namely, the cytosolic and
mitochondrial forms) can be divided into two classes.
 
Class I AATRSs contain a characteristic Rossman fold and are mostly
monomeric. At the primary structure level, two highly-conserved motifs
are observed, `HIGH' and `KMSKS' [2,3]; these are associated with the ATP-
binding site.
 
Class II AATRSs share an anti-parallel beta-sheet formation, flanked by
alpha-helices [3], and are mostly dimeric or multimeric.
 
Further distinction between the two classes is evident when the reaction
mechanisms are investigated. In reactions catalysed by the class I AATRSs,
the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in
class II reactions, the 3'-hydroxyl site is preferred.
 
Valyl-tRNA synthetase (EC 6.1.1.9 ) is specific to valine and belongs to
class I.
 
TRNASYNTHVAL is a 5-element fingerprint that provides a signature for 
valyl-tRNA synthetases. The fingerprint was derived from an initial
alignment of 9 sequences: the motifs were drawn from conserved regions
within the C-terminal portion of the alignment - motif 1 includes part
of the region encoded by PROSITE pattern AA_TRNA_LIGASE_I (PS00178). Two
iterations on OWL30.2 were required to reach convergence, at which point a
true set comprising 26 sequences was identified. Several partial matches
were also found: three of these are valine AATRSs from Plasmodium sp. that
fail to make significant matches with a number of motifs; three are 
fragments; and the remaining matches are closely related isoleucine AATRSs
from Methanobacterium.
 
An update on SPTR37_9f identified a true set of 27 sequences, and 3
partial matches.
Summary Information
  27 codes involving  5 elements
1 codes involving 4 elements
2 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
52727272727
401111
320022
200000
12345
True Positives
O14160        O53175        O58052        O67411        
O75005 O77443 O84304 SYV_ARATH
SYV_ARCFU SYV_BACST SYV_BACSU SYV_BORBU
SYV_ECOLI SYV_FUGRU SYV_HAEIN SYV_HELPY
SYV_HUMAN SYV_LACCA SYV_METJA SYV_METTH
SYV_MYCGE SYV_MYCPN SYV_NEUCR SYV_SYNY3
SYV_THETH SYV_TREPA SYV_YEAST
True Positive Partials
Codes involving 4 elements
Q23360
Codes involving 3 elements
Q26177 Q26178
Sequence Titles
O14160      PUTATIVE VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). 
O53175 VALYL-TRNA SYNTHETASE - MYCOBACTERIUM TUBERCULOSIS.
O58052 896AA LONG HYPOTHETICAL VALYL-TRNA SYNTHETASE - PYROCOCCUS HORIKOSHII.
O67411 VALYL-TRNA SYNTHETASE - AQUIFEX AEOLICUS.
O75005 VALYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O77443 VALYL TRNA SYNTHETASE - GIARDIA INTESTINALIS.
O84304 VALYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
SYV_ARATH VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
SYV_ARCFU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - ARCHAEOGLOBUS FULGIDUS.
SYV_BACST VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - BACILLUS STEAROTHERMOPHILUS.
SYV_BACSU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - BACILLUS SUBTILIS.
SYV_BORBU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
SYV_ECOLI VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - ESCHERICHIA COLI.
SYV_FUGRU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES).
SYV_HAEIN VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - HAEMOPHILUS INFLUENZAE.
SYV_HELPY VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYV_HUMAN VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - HOMO SAPIENS (HUMAN).
SYV_LACCA VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - LACTOBACILLUS CASEI.
SYV_METJA VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - METHANOCOCCUS JANNASCHII.
SYV_METTH VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
SYV_MYCGE VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - MYCOPLASMA GENITALIUM.
SYV_MYCPN VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - MYCOPLASMA PNEUMONIAE.
SYV_NEUCR VALYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - NEUROSPORA CRASSA.
SYV_SYNY3 VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
SYV_THETH VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
SYV_TREPA VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - TREPONEMA PALLIDUM.
SYV_YEAST VALYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

Q23360 SIMILARITY TO THE CARBOXYL TWO-THIRDS OF VALYL-TRNA SYNTHETASES - CAENORHABDITIS ELEGANS.

Q26177 GAM1 GENE - PLASMODIUM VIVAX.
Q26178 GAM1 GENE - PLASMODIUM VIVAX.
Scan History
OWL30_2    2  50   NSINGLE    
SPTR37_9f 2 33 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
FTIVIPPPNVTG SYV_BACST 42 42 -
YSVVIPPPNVTG SYV_BACSU 42 42 -
FCIPAPPPNVTG SYV_YEAST 183 183 -
FMMCIPPPNVTG SYV_HUMAN 337 337 -
YCVVIPPPNVTG SYV_SYNY3 39 39 -
FMMCIPPPNVTG SYV_FUGRU 286 286 -
FCLMMPPPNVTG SYV_HELPY 44 44 -
FVIFMPPPNVTG SYV_THETH 36 36 -
YIIDTPPPYPTG SYV_METJA 36 36 -

Motif 2 width=18
Element Seqn Id St Int Rpt
HPDDERYKHLIGKMVKLP SYV_BACST 236 182 -
HPEDERYKHLIGKTVILP SYV_BACSU 236 182 -
HPDDDRYKHLHGKFIQHP SYV_YEAST 394 199 -
HPKDTRYQHLKGKNVIHP SYV_HUMAN 550 201 -
NPHDERYAAMVGKTITLP SYV_SYNY3 233 182 -
HPSDSRYQHLKGKTVLHP SYV_FUGRU 497 199 -
NPNDERYKHLVGQKAILP SYV_HELPY 237 181 -
HPEDERYRHLLGKRARIP SYV_THETH 228 180 -
HPEDERYKHLIGKEFIVP SYV_METJA 227 179 -

Motif 3 width=14
Element Seqn Id St Int Rpt
RSGAVIEPYLSTQW SYV_BACST 351 97 -
RSGAVVEPYLSTQW SYV_BACSU 351 97 -
RSGDIIEPLLKPQW SYV_YEAST 511 99 -
RSKDVVEPLLRPQW SYV_HUMAN 665 97 -
RGKVPVEPLLSTQW SYV_SYNY3 348 97 -
RSKDIVEPLMKPQW SYV_FUGRU 612 97 -
RCHNVVEPYVSKQW SYV_HELPY 352 97 -
RCGTPIEYAIFPQW SYV_THETH 338 92 -
RCKTPIEIIVTEQW SYV_METJA 342 97 -

Motif 4 width=22
Element Seqn Id St Int Rpt
DPDVLDTWFSSALWPFSTMGWP SYV_BACST 445 80 -
DTDVLDTWFSSALWPFSTMGWP SYV_BACSU 445 80 -
DEDVLDTWFSSGLWPFSTLGWP SYV_YEAST 624 99 -
DEDVLDTWFSSGLFPLSILGWP SYV_HUMAN 783 104 -
DPDVLDTWFSSGLWPFSTMGWP SYV_SYNY3 460 98 -
DEDVLDTWFSSGINPFSILGWP SYV_FUGRU 730 104 -
DKDVLDTWFSSGLWAFSTLGWG SYV_HELPY 448 82 -
DEDVFDTWFSSALWPLSTLGWP SYV_THETH 441 89 -
ETDVLDTWMDSSITPMVITKWL SYV_METJA 448 92 -

Motif 5 width=19
Element Seqn Id St Int Rpt
YPTDVLVTGYDIIFFWVSR SYV_BACST 477 10 -
YPTDVLVTGYDIIFFWVSR SYV_BACSU 477 10 -
YPFSMLETGWDILFFWVTR SYV_YEAST 655 9 -
YPGTLLETGHDILFFWVAR SYV_HUMAN 814 9 -
YPTSTLVTGFDIIFFWVAR SYV_SYNY3 491 9 -
YPGTLLETGHDILFFWVAR SYV_FUGRU 761 9 -
YPNTTLITGFDILFFWVAR SYV_HELPY 485 15 -
YPGDVLVTGYDILFLWVSR SYV_THETH 472 9 -
YPVQLRPQGHDIIRTWAFY SYV_METJA 479 9 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
FTIVIPPPNVTG SYV_BACST 42 42 -
YSVVIPPPNVTG SYV_BACSU 42 42 -
YSIVLPPPNVTG O53175 36 36 -
FVIVLPPPNVTG SYV_ARATH 170 170 -
FCIPAPPPNVTG SYV_YEAST 183 183 -
YCIAIPPPNVTG SYV_HAEIN 41 41 -
FSMVAPPPNVTG SYV_BORBU 38 38 -
FSVVIPPPNVTG O67411 36 36 -
FMMCIPPPNVTG SYV_HUMAN 337 337 -
YSIVMPPPNVTG O84304 40 40 -
FCIMIPPPNVTG SYV_ECOLI 35 35 -
YCVVIPPPNVTG SYV_SYNY3 39 39 -
FMMCIPPPNVTG SYV_FUGRU 286 286 -
FVIAIPPPNITG SYV_TREPA 62 62 -
FVITSPPPNVTG O75005 132 132 -
YSIVIPPPNVTG SYV_LACCA 61 61 -
FCLMMPPPNVTG SYV_HELPY 44 44 -
FVIFMPPPNVTG SYV_THETH 36 36 -
FVIPLPPPNVTG SYV_NEUCR 172 172 -
FTLLIPPPNVTG O77443 97 97 -
FPILLPPPNITG O14160 2 2 -
FTAILPPPNLTG SYV_MYCGE 39 39 -
FTAILPPPNLTG SYV_MYCPN 39 39 -
YIIDTPPPYPTG SYV_ARCFU 36 36 -
YIIDTPPPYPTG SYV_METJA 36 36 -
YIIDTPPPYPTG SYV_METTH 59 59 -
YAIDTPPPFTSG O58052 41 41 -

Motif 2 width=18
Element Seqn Id St Int Rpt
HPDDERYKHLIGKMVKLP SYV_BACST 236 182 -
HPEDERYKHLIGKTVILP SYV_BACSU 236 182 -
HPDDERYRHLVGTSLAHP O53175 231 183 -
HPDDARYKHLHGKFAVHP SYV_ARATH 380 198 -
HPDDDRYKHLHGKFIQHP SYV_YEAST 394 199 -
HPEDERYQSLIGKTVVLP SYV_HAEIN 242 189 -
NPNDERYKSLVGKEVTIP SYV_BORBU 231 181 -
NPNDDRYKHLVGKRARLP O67411 235 187 -
HPKDTRYQHLKGKNVIHP SYV_HUMAN 550 201 -
SPEDLRYSHLIGAKVVVP O84304 235 183 -
NPEDPRYKDLIGKYVILP SYV_ECOLI 236 189 -
NPHDERYAAMVGKTITLP SYV_SYNY3 233 182 -
HPSDSRYQHLKGKTVLHP SYV_FUGRU 497 199 -
HPDDARYQSLIGRKVCVP SYV_TREPA 273 199 -
HPQDPRYKHLHGKFVKHP O75005 343 199 -
HPGDERYKDMVGTELILP SYV_LACCA 255 182 -
NPNDERYKHLVGQKAILP SYV_HELPY 237 181 -
HPEDERYRHLLGKRARIP SYV_THETH 228 180 -
NPEDPRYTHLVGKFARHP SYV_NEUCR 383 199 -
HPRDHRYTDLHGRCLFHP O77443 377 268 -
SPHDERYKKYVGRFVKHP O14160 211 197 -
NPKDKRYTNFWNKLVVNP SYV_MYCGE 234 183 -
HPKDKHYHSFVKQKVVNP SYV_MYCPN 234 183 -
HPDDERNKHLIGKKVRVP SYV_ARCFU 222 174 -
HPEDERYKHLIGKEFIVP SYV_METJA 227 179 -
HPDDERFREFEDKLIEVP SYV_METTH 250 179 -
HPDDERYKHLVGKKVKLP O58052 230 177 -

Motif 3 width=14
Element Seqn Id St Int Rpt
RSGAVIEPYLSTQW SYV_BACST 351 97 -
RSGAVVEPYLSTQW SYV_BACSU 351 97 -
RSGEPIEPRLSLQW O53175 347 98 -
RTNDVIEPMIKPQW SYV_ARATH 497 99 -
RSGDIIEPLLKPQW SYV_YEAST 511 99 -
RGGVPIEPMLTDQW SYV_HAEIN 375 115 -
RSGEVIEPYLSTQW SYV_BORBU 347 98 -
RCKTVIEPMVSVQW O67411 362 109 -
RSKDVVEPLLRPQW SYV_HUMAN 665 97 -
RSGAIIEPYLSKQW O84304 350 97 -
RGGVVIEPMLTDQW SYV_ECOLI 369 115 -
RGKVPVEPLLSTQW SYV_SYNY3 348 97 -
RSKDIVEPLMKPQW SYV_FUGRU 612 97 -
RCEAVIEPYLSLQW SYV_TREPA 389 98 -
KTSDIIEPVMKPQW O75005 459 98 -
RTGVQVEARLSTQW SYV_LACCA 370 97 -
RCHNVVEPYVSKQW SYV_HELPY 352 97 -
RCGTPIEYAIFPQW SYV_THETH 338 92 -
KSKDVIEPMMTEQW SYV_NEUCR 498 97 -
RSGDILEPMVKPQW O77443 506 111 -
RTGDVIEPVMVPQW O14160 327 98 -
RSGTVVEPMLSKQW SYV_MYCGE 349 97 -
RSDTVVEPLLSKQW SYV_MYCPN 349 97 -
RCKTPVEIIPAEQW SYV_ARCFU 337 97 -
RCKTPIEIIVTEQW SYV_METJA 342 97 -
RCKTPIEILVKKQW SYV_METTH 365 97 -
SCMAPIELLPKKQW O58052 348 100 -

Motif 4 width=22
Element Seqn Id St Int Rpt
DPDVLDTWFSSALWPFSTMGWP SYV_BACST 445 80 -
DTDVLDTWFSSALWPFSTMGWP SYV_BACSU 445 80 -
DPDVLDTWFSSALWPFSTLGWP O53175 439 78 -
DPDVLDTWFSSGLFPLSVLGWP SYV_ARATH 615 104 -
DEDVLDTWFSSGLWPFSTLGWP SYV_YEAST 624 99 -
DEDVLDTWFSSGLWTFSTLGWP SYV_HAEIN 475 86 -
DPDVLDTWFSSWLWPFSSLGWP SYV_BORBU 445 84 -
ERDVLDTWFSSALWPFGVFGWP O67411 721 345 -
DEDVLDTWFSSGLFPLSILGWP SYV_HUMAN 783 104 -
DPDVLDTWFSSGLWPLTCFGWP O84304 449 85 -
DEDVLDTWFSSALWTFSTLGWP SYV_ECOLI 469 86 -
DPDVLDTWFSSGLWPFSTMGWP SYV_SYNY3 460 98 -
DEDVLDTWFSSGINPFSILGWP SYV_FUGRU 730 104 -
DPDVLDTWFSSWLWPFSTLGWP SYV_TREPA 487 84 -
DEDVLDTWFSSGLWPFSTLGWP O75005 573 100 -
DPDVLDTWFSSALWPFSTMGWP SYV_LACCA 465 81 -
DKDVLDTWFSSGLWAFSTLGWG SYV_HELPY 448 82 -
DEDVFDTWFSSALWPLSTLGWP SYV_THETH 441 89 -
DPDCLDTWFSSGLWPMAILGWP SYV_NEUCR 612 100 -
DDDVTDTWFSSGLFPFSCFADS O77443 627 107 -
DSDVLDTWFSSALLPLSAFGWP O14160 423 82 -
SKDVLDTWFSSSLWPLICLNWE SYV_MYCGE 439 76 -
STDVLDTWFSSSLWPLICLDWH SYV_MYCPN 439 76 -
ETDVLDTWMDSSITPLMICGWP SYV_ARCFU 443 92 -
ETDVLDTWMDSSITPMVITKWL SYV_METJA 448 92 -
EEDVLDTWMDSSISPLSVAGWP SYV_METTH 472 93 -
VTDVLDCWVDSSITPLIITKWH O58052 455 93 -

Motif 5 width=19
Element Seqn Id St Int Rpt
YPTDVLVTGYDIIFFWVSR SYV_BACST 477 10 -
YPTDVLVTGYDIIFFWVSR SYV_BACSU 477 10 -
YPTSVLVTGYDILFFWVAR O53175 470 9 -
YPTSVLETGHDILFFWVAR SYV_ARATH 646 9 -
YPFSMLETGWDILFFWVTR SYV_YEAST 655 9 -
HPTDVLITGFDIIFFWVAR SYV_HAEIN 506 9 -
YPTNTLITAYDIIFFWVAR SYV_BORBU 476 9 -
YPTDLLVTGFDIIFFWVAR O67411 752 9 -
YPGTLLETGHDILFFWVAR SYV_HUMAN 814 9 -
YPTAVLVTGHDILFFWVTR O84304 481 10 -
HPTSVMVSGFDIIFFWIAR SYV_ECOLI 500 9 -
YPTSTLVTGFDIIFFWVAR SYV_SYNY3 491 9 -
YPGTLLETGHDILFFWVAR SYV_FUGRU 761 9 -
YPTSAVITAYDIIFFWVAR SYV_TREPA 518 9 -
YPTTLMETGWDILFFWIAR O75005 604 9 -
YPTDTLVTGYDIIPFWVAR SYV_LACCA 497 10 -
YPNTTLITGFDILFFWVAR SYV_HELPY 485 15 -
YPGDVLVTGYDILFLWVSR SYV_THETH 472 9 -
FPTSMLETGWDILFFWVSR SYV_NEUCR 644 10 -
YPGSVLETGNDIIFFWVAR O77443 656 7 -
QPLPFIESGQDILFFWIAR O14160 450 5 -
HETELLVTGYDILFFWVLR SYV_MYCGE 466 5 -
VPTDLLVTGYDILFFWVLR SYV_MYCPN 466 5 -
YPTHLRPQGHDIIRTWAFY SYV_ARCFU 469 4 -
YPVQLRPQGHDIIRTWAFY SYV_METJA 479 9 -
FPADLRPQGHDIIRTWAFY SYV_METTH 501 7 -
FPTALRPQGTDIIRTWAFY O58052 493 16 -