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PR00996

Identifier
CHERMTFRASE  [View Relations]  [View Alignment]  
Accession
PR00996
No. of Motifs
6
Creation Date
23-SEP-1998  (UPDATE 14-JUN-1999)
Title
Glutamate methyltransferase family signature
Database References

PFAM; PF00891 Methyltransf
INTERPRO; IPR000780
Literature References
1. LODISH, H., BALTIMORE, D., BERK, A., ZIPURSKY, S.L., MATSUDAIRA, P. AND
DARNELL, J.
Microfilaments: Cell Motility and Control of Cell Shape.
IN MOLECULAR CELL BIOLOGY, SCIENTIFIC AMERICAN BOOKS (NEW YORK), 1995,
PP.1044-1045.
 
2. DJORDJEVIC, S. AND STOCK, A.M.
Crystal structure of the chemotaxis receptor methyltransferase CheR suggests
a conserved structural motif for binding S-adenosylmethionine.
STRUCTURE 5 545-558 (1997). 
 
3. DJORDJEVIC, S. AND STOCK, A.M.
Chemotaxis receptor recognition by protein methyltransferase CheR.
NAT.STRUCT.BIOL. 5 446-450 (1998). 

Documentation
Flagellated bacteria swim towards favourable chemicals and away from
deleterious ones. Sensing of chemoeffector gradients involves chemotaxis
receptors, transmembrane (TM) proteins that detect stimuli through their 
periplasmic domains and transduce the signals via their cytoplasmic domains 
[1,2]. Signalling outputs from these receptors are influenced both by the
binding of the chemoeffector ligand to their periplasmic domains and by 
methylation of specific glutamate residues on their cytoplasmic domains.
Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyl-
transferase [2], which reversibly methylates specific glutamate residues
within a coiled coil region, to form gamma-glutamyl methyl ester residues
[2,3]: 
 
 S-Adenosyl-L-Methionine	       S-Adenosyl-L-Homocysteine
	  +		       =		  +
   Protein L-Glutamate		    Protein L-Glutamate Methyl Ester
 
The structure of the S.typhimurium chemotaxis receptor methyltransferase
CheR, bound to S-adenosylhomocysteine, has been determined to a resolution
of 2.0A [2]. The structure reveals CheR to be a two-domain protein, with a 
smaller N-terminal helical domain linked via a single polypeptide connection
to a larger C-terminal alpha/beta domain [2]. The C-terminal domain has the
characteristics of a nucleotide-binding fold, with an insertion of a small
anti-parallel beta-sheet subdomain [2]. The S-adenosylhomocysteine-binding 
site is formed mainly by the large domain, with contributions from residues
within the N-terminal domain and the linker region [2]. 
 
CHERMTFRASE is a 6-element fingerprint that provides a signature for the
cheR glutamate methyltransferase family. The fingerprint was derived from 
an initial alignment of 10 sequences: the motifs were drawn from short
conserved regions spanning the full alignment length. Two iterations on
OWL30.2 were required to reach convergence, at which point a true set
comprising 13 sequences was identified. Several partial matches were also
found, all of which are fragments or homologues that fail to match one or
more motifs.
 
An update on SPTR37_9f identified a true set of 20 sequences, and 8
partial matches.
Summary Information
  20 codes involving  6 elements
0 codes involving 5 elements
1 codes involving 4 elements
1 codes involving 3 elements
5 codes involving 2 elements
Composite Feature Index
6202020202020
5000000
4001111
3001011
2202123
123456
True Positives
CHER_BACSU    CHER_ECOLI    CHER_SALTY    FRZF_MYXXA    
O29225 O32009 O33557 O51069
O51375 O58194 O83638 O85127
O87131 O87716 P72254 Q51346
Q52882 Q53129 Q57508 YPEB_CAMJE
True Positive Partials
Codes involving 4 elements
Q51774
Codes involving 3 elements
YH19_RHOCA
Codes involving 2 elements
O54158 O85748 Q18331 YCF2_MARPO
YRP3_GIALA
Sequence Titles
CHER_BACSU  CHEMOTAXIS PROTEIN METHYLTRANSFERASE (EC 2.1.1.80) - BACILLUS SUBTILIS. 
CHER_ECOLI CHEMOTAXIS PROTEIN METHYLTRANSFERASE (EC 2.1.1.80) - ESCHERICHIA COLI.
CHER_SALTY CHEMOTAXIS PROTEIN METHYLTRANSFERASE (EC 2.1.1.80) - SALMONELLA TYPHIMURIUM.
FRZF_MYXXA PROTEIN METHYLTRANSFERASE FRZF (EC 2.1.1.80) - MYXOCOCCUS XANTHUS.
O29225 CHEMOTAXIS PROTEIN METHYLTRANSFERASE (CHER) - ARCHAEOGLOBUS FULGIDUS.
O32009 METHYL-ACCEPTING CHEMOTAXIS PROTEINS (MCPS) METHYLTRANSFERASE (EC 2.1.1.80) (PROTEIN-GLUTAMATE O-METHYLTRANSFERASE) (METHYL-ACCEPTING CHEMOTAXIS PROTEIN O-METHYLTRANSFERASE) - BACILLUS SUBTILIS.
O33557 METHYLTRANSFERASE - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
O51069 CHEMOTAXIS PROTEIN METHYLTRANSFERASE (CHER-1) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O51375 CHEMOTAXIS PROTEIN METHYLTRANSFERASE (CHER-2) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O58194 280AA LONG HYPOTHETICAL CHEMOTAXIS PROTEIN METHYLTRANSFERASE - PYROCOCCUS HORIKOSHII.
O83638 CHEMOTAXIS PROTEIN METHYLTRANSFERASE (CHER) - TREPONEMA PALLIDUM.
O85127 CHER HOMOLOG - AGROBACTERIUM TUMEFACIENS.
O87131 CHER - PSEUDOMONAS AERUGINOSA.
O87716 CHER - CAULOBACTER CRESCENTUS.
P72254 CHER - RHODOSPIRILLUM CENTENUM.
Q51346 PAO1 (PILK) - PSEUDOMONAS AERUGINOSA.
Q52882 CHER - RHIZOBIUM MELILOTI.
Q53129 CHEMOTAXIS OPERON DNA - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
Q57508 CHEMOTAXIS METHYL TRANSFERASE - VIBRIO ANGUILLARUM.
YPEB_CAMJE HYPOTHETICAL 31.0 KD PROTEIN IN PEB1B 5'REGION (ORFB) - CAMPYLOBACTER JEJUNI.

Q51774 METHYLTRANSFERASE - PSEUDOMONAS FLUORESCENS.

YH19_RHOCA HYPOTHETICAL 104.1 KD PROTEIN IN HYPE 3'REGION (ORF19) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).

O54158 PUTATIVE METHYLTRANSFERASE - STREPTOMYCES COELICOLOR.
O85748 CHEW - TREPONEMA DENTICOLA.
Q18331 SIMILAR TO GUANYLATE CYCLASE RECEPTOR. NCBI GI: 1208828 - CAENORHABDITIS ELEGANS.
YCF2_MARPO HYPOTHETICAL 259 KD PROTEIN (ORF 2136) - MARCHANTIA POLYMORPHA (LIVERWORT).
YRP3_GIALA HYPOTHETICAL 59.1 KD PROTEIN IN RPOA3 5'REGION - GIARDIA LAMBLIA (GIARDIA INTESTINALIS).
Scan History
OWL30_2    2  200  NSINGLE    
SPTR37_9f 4 224 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
RESYLRRRIELRMK E69379 24 24 -
KKLLIESRLSSLLK H70104 38 38 -
NKFVLQSRVNDAVR E70151 28 28 -
RRTFLQASLTARMR S61498 39 39 -
KASLVYSRLSKHIR S61836 48 48 -
KEPLVYARLAKRLR S70183 41 41 -
KQYLVRSRLSPLVA S70895 30 30 -
KEAQMKRRLTSLYE CHER_BACSU 23 23 -
KRDMVYNRLVRRLR CHER_SALTY 46 46 -
KRDMVYNRLVRRLR CHER_ECOLI 46 46 -

Motif 2 width=13
Element Seqn Id St Int Rpt
LINTITINVTEFM E69379 62 24 -
FISSMTTNTTRFF S70183 80 25 -
AVDAMTTNETLWF S70895 69 25 -
MLSHLTTNFTRFF S61836 87 25 -
LIDKISTNHTYFF H70104 77 25 -
FLDLVTTNLTRFF E70151 65 23 -
LLDRLTVQETRFF S61498 79 26 -
TLDRMTINVSEFY CHER_BACSU 60 23 -
FINALTTNLTAFF CHER_SALTY 85 25 -
FINSLTTNLTAFF CHER_ECOLI 85 25 -

Motif 3 width=21
Element Seqn Id St Int Rpt
KIWSAACSTGEEPYTLAMLLD CHER_BACSU 96 23 -
RVWSAAASTGEEPYSIAMTLA CHER_ECOLI 118 20 -
RFWSAGCSSGEEPFSMAITLL S70183 120 27 -
RIWSAACSDGQEPYSIALTVL S61836 127 27 -
KIWSAASSSGQEPYSMAMTVL S70895 106 24 -
RAWSAGCSCGEEPYSIAISIL E69379 104 29 -
RIWSAGCSSGEEPYTIAMMLK H70104 119 29 -
IIWSAGCSTGEEPYSLAFVLK E70151 107 29 -
ALWSVGCSSGEEPYSLAMCAA S61498 118 26 -
RVWSAAASTGEEPYSIAITLA CHER_SALTY 118 20 -

Motif 4 width=17
Element Seqn Id St Int Rpt
ASDIDTEVLEKARSGIY CHER_SALTY 152 13 -
ATDIDRKILGRAQAGWF S70183 155 14 -
ATDIDPKILALARAGAY S61836 162 14 -
ATDISASMLDMCKAGIY S70895 143 16 -
ATDIDDACLEMAREGFY E69379 137 12 -
ATDISISVLNEAREGIY H70104 155 15 -
ASDLSLKSLMIAKEGYY E70151 140 12 -
GTDISLHALQRARQANY S61498 154 15 -
ASDIDTEVLEKARSGIY CHER_ECOLI 152 13 -
ATDIDEKALEKAKKGVY CHER_BACSU 128 11 -

Motif 5 width=15
Element Seqn Id St Int Rpt
FDVIFCRNVVIYFDE S61836 233 54 -
MDVIFCQNLLIYFRR S61498 223 52 -
FDVIFCRNVAIYFDP S70183 224 52 -
IDVVFCRNVLIYFDE E70151 205 48 -
FDAIFCRNVMIYFDQ CHER_ECOLI 224 55 -
FDAIFCRNVMIYFDK CHER_SALTY 224 55 -
FDLIVCRNVFIYFTE CHER_BACSU 195 50 -
FDLIFCRNVMIYFDE H70104 224 52 -
LDIVFCRNVMIYFSE E69379 204 50 -
FDIIFCRNVLIYFSP S70895 212 52 -

Motif 6 width=24
Element Seqn Id St Int Rpt
NLANKFNSYLKKDSYLLIGHSETI H70104 243 4 -
EILNRLAERLAPGGLLVIGVGEVV S61498 242 4 -
KVLNQMASSLNPGGYLLLGASESL S70895 231 4 -
KIWSRFAGVLDNGGHLYIGHSERV S61836 252 4 -
RIWRGFASTLAPGGHLFIGHSERL S70183 243 4 -
DILRRFVPLLKPDGLLFAGHSENF CHER_SALTY 243 4 -
ELYLKMAHSLKKNGVLFVGSTEQI CHER_BACSU 214 4 -
EILRRFVPLLKPDGLLFAGHSENF CHER_ECOLI 243 4 -
KVVNDFYNALVDGGYLVIGRSETL E69379 223 4 -
KVLKKFYNNMSKNSYLFIGHSESL E70151 224 4 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
KASLVYSRLSKHIR O85127 48 48 -
KASLVYSRLSKHIR Q52882 48 48 -
KRDMVYNRLVRRLR CHER_ECOLI 46 46 -
KRDMVYNRLVRRLR CHER_SALTY 46 46 -
KATLVYSRLAKRLR O87716 46 46 -
KEPLVYARLAKRLR Q53129 41 41 -
KKLLIESRLSSLLK O51069 38 38 -
KQYLVRSRLSPLVA Q57508 30 30 -
KQYLVSSRLNKLME O87131 27 27 -
NRSVLESRIRSRLR O83638 51 51 -
KAYLLESRLMPIAR P72254 25 25 -
KEAQMKRRLTSLYE O32009 23 23 -
KEAQMKRRLTSLYE CHER_BACSU 23 23 -
NKFVLQSRVNDAVR O51375 28 28 -
KDSYLQRRIRARMR O58194 27 27 -
RRQMIESRLRPRIA O33557 29 29 -
RESYLRRRIELRMK O29225 24 24 -
RRTFLQASLTARMR Q51346 39 39 -
PDGFHSLRLALSAR FRZF_MYXXA 26 26 -
KKNILALKLNKFLE YPEB_CAMJE 30 30 -

Motif 2 width=13
Element Seqn Id St Int Rpt
MLSHLTTNFTRFF O85127 87 25 -
MLSHLTTNFTRFF Q52882 87 25 -
FINSLTTNLTAFF CHER_ECOLI 85 25 -
FINALTTNLTAFF CHER_SALTY 85 25 -
MLRALTTNVTRFF O87716 85 25 -
FISSMTTNTTRFF Q53129 80 25 -
LIDKISTNHTYFF O51069 77 25 -
AVDAMTTNETLWF Q57508 69 25 -
VVDAMTTNETLWF O87131 65 24 -
LLDSVTTNLTRFF O83638 88 23 -
ITEAMTTNESSFF P72254 64 25 -
TLDRMTINVSEFY O32009 60 23 -
TLDRMTINVSEFY CHER_BACSU 60 23 -
FLDLVTTNLTRFF O51375 65 23 -
LLLTIAINVTEFF O58194 64 23 -
VIDLLTTNKTDFY O33557 69 26 -
LINTITINVTEFM O29225 62 24 -
LLDRLTVQETRFF Q51346 79 26 -
LLPLVTVGHTEFF FRZF_MYXXA 67 27 -
TLDFVTIGETYFL YPEB_CAMJE 67 23 -

Motif 3 width=21
Element Seqn Id St Int Rpt
RIWSAACSDGQEPYSIALTVL O85127 127 27 -
RIWSAACSDGQEPYSIALTVL Q52882 127 27 -
RVWSAAASTGEEPYSIAMTLA CHER_ECOLI 118 20 -
RVWSAAASTGEEPYSIAITLA CHER_SALTY 118 20 -
RLWSAASSSGQEPYSMAFTVL O87716 125 27 -
RFWSAGCSSGEEPFSMAITLL Q53129 120 27 -
RIWSAGCSSGEEPYTIAMMLK O51069 119 29 -
KIWSAASSSGQEPYSMAMTVL Q57508 106 24 -
RIWSAACSSGQEPYSLSMAID O87131 104 26 -
TVWSAGCSTGEEPYTIAMLLK O83638 130 29 -
RIWSAACSSGQEAYSLLMTLN P72254 104 27 -
KIWSAACSTGEEPYTLAMLLD O32009 96 23 -
KIWSAACSTGEEPYTLAMLLD CHER_BACSU 96 23 -
IIWSAGCSTGEEPYSLAFVLK O51375 107 29 -
KIWSAACSTGQEPYSIAMTLY O58194 106 29 -
KIWSAASSEGAEAYTAAIVLA O33557 110 28 -
RAWSAGCSCGEEPYSIAISIL O29225 104 29 -
ALWSVGCSSGEEPYSLAMCAA Q51346 118 26 -
SIWSAGCATGEEPYSLAMVLA FRZF_MYXXA 108 28 -
NILSAPCSSGEEVYSLALLAA YPEB_CAMJE 100 20 -

Motif 4 width=17
Element Seqn Id St Int Rpt
ATDIDPKILAQARAGVY O85127 162 14 -
ATDIDPKILALARAGAY Q52882 162 14 -
ASDIDTEVLEKARSGIY CHER_ECOLI 152 13 -
ASDIDTEVLEKARSGIY CHER_SALTY 152 13 -
GTDIDTNVLATGRAAVY O87716 160 14 -
ATDIDRKILGRAQAGWF Q53129 155 14 -
ATDISISVLNEAREGIY O51069 155 15 -
ATDISASMLDMCKAGIY Q57508 143 16 -
ATDLSGSMLTAAKAGEY O87131 142 17 -
ASDLSLKSLLVARQGYY O83638 163 12 -
GTDISAEMVAKAKAGLY P72254 139 14 -
ATDIDEKALEKAKKGVY O32009 128 11 -
ATDIDEKALEKAKKGVY CHER_BACSU 128 11 -
ASDLSLKSLMIAKEGYY O51375 140 12 -
ATDIDKEALQIAMRGEY O58194 142 15 -
GTDISHRMLERARRAIY O33557 145 14 -
ATDIDDACLEMAREGFY O29225 137 12 -
GTDISLHALQRARQANY Q51346 154 15 -
ATDLNLAAVEAAKQGRF FRZF_MYXXA 141 12 -
GVDINSSVIEKAKLGKY YPEB_CAMJE 131 10 -

Motif 5 width=15
Element Seqn Id St Int Rpt
FDVIFCRNVVIYFDE O85127 233 54 -
FDVIFCRNVVIYFDE Q52882 233 54 -
FDAIFCRNVMIYFDQ CHER_ECOLI 224 55 -
FDAIFCRNVMIYFDK CHER_SALTY 224 55 -
FDAIFCRNVVIYFDE O87716 231 54 -
FDVIFCRNVAIYFDP Q53129 224 52 -
FDLIFCRNVMIYFDE O51069 224 52 -
FDIIFCRNVLIYFSP Q57508 212 52 -
FDMVFCRNVLIYFSA O87131 211 52 -
VDVLFCRNVLIYFDE O83638 229 49 -
FDVIFCRNVLIYFDQ P72254 207 51 -
FDLIVCRNVFIYFTE O32009 195 50 -
FDLIVCRNVFIYFTE CHER_BACSU 195 50 -
IDVVFCRNVLIYFDE O51375 205 48 -
FDVIFIRNVLIYMSK O58194 210 51 -
VDVIFLRNVLIYFGP O33557 218 56 -
LDIVFCRNVMIYFSE O29225 204 50 -
MDVIFCQNLLIYFRR Q51346 223 52 -
LDLILCRNVIIYFDL FRZF_MYXXA 211 53 -
FDIIASRNMIIYFDH YPEB_CAMJE 200 52 -

Motif 6 width=24
Element Seqn Id St Int Rpt
RIWSRFAGLLPEGGHLYIGHSERV O85127 252 4 -
KIWSRFAGVLDNGGHLYIGHSERV Q52882 252 4 -
EILRRFVPLLKPDGLLFAGHSENF CHER_ECOLI 243 4 -
DILRRFVPLLKPDGLLFAGHSENF CHER_SALTY 243 4 -
RVWNRFAPLVAPGGRLYVGHSERV O87716 250 4 -
RIWRGFASTLAPGGHLFIGHSERL Q53129 243 4 -
NLANKFNSYLKKDSYLLIGHSETI O51069 243 4 -
KVLNQMASSLNPGGYLLLGASESL Q57508 231 4 -
DILLRIHGTLKPGGYLFLGASEAL O87131 230 4 -
AVIERFWDAMSAHSFLFIGHSESL O83638 248 4 -
KVLEAMARMLPPDGVLYLGGAETV P72254 226 4 -
ELYLKMAHSLKKNGVLFVGSTEQI O32009 214 4 -
ELYLKMAHSLKKNGVLFVGSTEQI CHER_BACSU 214 4 -
KVLKKFYNNMSKNSYLFIGHSESL O51375 224 4 -
DIFRKLYDSLEDHGYLILGKTETI O58194 229 4 -
AVIARMAGHLRPGGYLMVGHSESM O33557 237 4 -
KVVNDFYNALVDGGYLVIGRSETL O29225 223 4 -
EILNRLAERLAPGGLLVIGVGEVV Q51346 242 4 -
GLMDRFLAALRPGGLLFLGYSESL FRZF_MYXXA 230 4 -
KLMERFHRILNDKGRLYVGNADLI YPEB_CAMJE 219 4 -