Identifier | TRNASYNTHARG  [View Relations]  [View Alignment]  
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Accession | PR01038 |
No. of Motifs | 4 |
Creation Date | 21-DEC-1998  (UPDATE 10-JUN-1999) |
Title | Arginyl-tRNA synthetase signature |
Database References | PRINTS; PR90000 TRNASYNTH; PR90001 TRNASYNTHCLI PROSITE; PS00178 AA_TRNA_LIGASE_I BLOCKS; BL00178 PFAM; PF00750 tRNA-synt_1d INTERPRO; IPR001278 |
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).
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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.
Arginyl-tRNA synthetase (EC 6.1.1.19) is specific to arginine and belongs to
class I.
TRNASYNTHARG is a 4-element fingerprint that provides a signature for the
arginyl-tRNA synthetase. The fingerprint was derived from an initial
alignment of 17 sequences: the motifs were drawn from conserved regions
mostly confined to the N-terminal portion of the alignment - motifs 1 and 2
hinge on the initial histidine in the conserved 'HIGH' region, spanning the
region encoded by PROSITE pattern AA_TRNA_LIGASE_I (PS00178). Two iterations
on OWL31.1 were required to reach convergence, at which point a true set
comprising 28 sequences was identified. Several partial matches were also
found, all of which are arginyl-tRNA synthetase fragments.
An update on SPTR37_9f identified a true set of 27 sequences, and 1
partial match.
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Summary Information | 27 codes involving 4 elements 0 codes involving 3 elements 1 codes involving 2 elements
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Composite Feature Index | |
True Positives | O23246 O23247 O59147 O67068 O74781 O84460 SYRC_YEAST SYRM_YEAST SYR_ARCFU SYR_BACSU SYR_BORBU SYR_BRELA SYR_CAEEL SYR_CORGL SYR_CRILO SYR_ECOLI SYR_HAEIN SYR_HELPY SYR_HUMAN SYR_METJA SYR_METTH SYR_MYCGE SYR_MYCLE SYR_MYCPN SYR_MYCTU SYR_SYNY3 SYR_TREPA |
True Positive Partials | Codes involving 2 elements Q18316 |
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Sequence Titles | O23246 ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). O23247 ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). O59147 629AA LONG HYPOTHETICAL ARGINYL-TRNA SYNTHETASE - PYROCOCCUS HORIKOSHII. O67068 ARGINYL-TRNA SYNTHETASE - AQUIFEX AEOLICUS. O74781 PUTATIVE ARGINYL-TRNA SYNTHETASE, CYTOPLASMIC - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). O84460 ARGINYL TRNA TRANSFERASE - CHLAMYDIA TRACHOMATIS. SYRC_YEAST PROBABLE ARGINYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.19) (ARGININE- -TRNA LIGASE) (ARGRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). SYRM_YEAST ARGINYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). SYR_ARCFU ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - ARCHAEOGLOBUS FULGIDUS. SYR_BACSU ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - BACILLUS SUBTILIS. SYR_BORBU ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE). SYR_BRELA ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - BREVIBACTERIUM LACTOFERMENTUM. SYR_CAEEL PROBABLE ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - CAENORHABDITIS ELEGANS. SYR_CORGL POSSIBLE ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - CORYNEBACTERIUM GLUTAMICUM (BREVIBACTERIUM FLAVUM). SYR_CRILO ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - CRICETULUS LONGICAUDATUS (LONG-TAILED HAMSTER) (CHINESE HAMSTER). SYR_ECOLI ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - ESCHERICHIA COLI. SYR_HAEIN ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - HAEMOPHILUS INFLUENZAE. SYR_HELPY ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI). SYR_HUMAN ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - HOMO SAPIENS (HUMAN). SYR_METJA ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - METHANOCOCCUS JANNASCHII. SYR_METTH ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - METHANOBACTERIUM THERMOAUTOTROPHICUM. SYR_MYCGE ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - MYCOPLASMA GENITALIUM. SYR_MYCLE ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - MYCOBACTERIUM LEPRAE. SYR_MYCPN ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - MYCOPLASMA PNEUMONIAE. SYR_MYCTU ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - MYCOBACTERIUM TUBERCULOSIS. SYR_SYNY3 ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803). SYR_TREPA ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19) (ARGININE--TRNA LIGASE) (ARGRS) - TREPONEMA PALLIDUM. Q18316 SIMILAR TO ARGINYL-TRNA SYNTHETASE - CAENORHABDITIS ELEGANS.
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Scan History | OWL31_1 2 100 NSINGLE SPTR37_9f 2 30 NSINGLE
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Initial Motifs | Motif 1 width=16 Element Seqn Id St Int Rpt RVQVEFVSANPTGDLH SYR_BACSU 124 124 - QINLEFVSANPTGPIH SYR_MYCLE 122 122 - KIILEHTSANPNGPLH SYR_METJA 116 116 - RIMVEFSSPNTNKPLH A71277 124 124 - KIILEFSSPNTNKPLH A70174 125 125 - KVLIEWVSANPTGELH SYR_MYCPN 105 105 - KIFLEFVSANPTGPLH SYR_HELPY 111 111 - TIVVDYSAPNVAKEMH SYR_ECOLI 114 114 - RIVVDFSSPNIAKEMH SYR_SYNY3 118 118 - RVLVDFSSPNIAKEMH SYR_CAEEL 245 245 - KVIVDFSSPNIAKEMH SYR_HUMAN 193 193 - KVIVDFSSPNIAKEMH SYR_CRILO 194 194 - KVVVEFSSPNIAKPFH SYRM_YEAST 180 180 - TVVIDYSSPNVAKEMH SYR_HAEIN 114 114 - KVNLEFVSANPTGPIH SYR_MYCTU 122 122 - DVNLEFVSANPTGPIH SYR_BRELA 122 122 - DVNLEFVSANPTGPIH SYR_CORGL 122 122 - Motif 2 width=17 Element Seqn Id St Int Rpt HVGHLRSTIIGESMSRL SYR_CRILO 209 -1 - HVGHLRNDVIGESLSRI A70174 140 -1 - HVGHLRNNAIGESLSRI A71277 139 -1 - HVGHLRSTIIGDCLARV SYR_SYNY3 133 -1 - HVGHLRSTIIGDSICRL SYR_CAEEL 260 -1 - HVGHLRSTIIGESISRL SYR_HUMAN 208 -1 - HAGHLRSTIIGGFLSNL SYRM_YEAST 195 -1 - HVGHLRSTIIGDAVART SYR_HAEIN 129 -1 - HIGGTRWAAVGDALGRL SYR_MYCTU 137 -1 - HLGGTRWAAVGDSLGRV SYR_BRELA 137 -1 - HLGGTRWAAVGDSLGRV SYR_CORGL 137 -1 - HLGHARGAAVGDSLCNV SYR_BACSU 139 -1 - HIGGTRWAAVGDALGRL SYR_MYCLE 137 -1 - HIGHLRNAIIGDCLKRI SYR_METJA 131 -1 - HVGHLRSTIIGDAAVRT SYR_ECOLI 129 -1 - HIGHARGAVFGDSLAKI SYR_HELPY 126 -1 - HLGHVRNAFFGHVLNNL SYR_MYCPN 120 -1 - Motif 3 width=14 Element Seqn Id St Int Rpt VLCEYYVNDMGSQI SYR_HELPY 150 7 - TVREYWVNDYGQQA SYR_MYCPN 144 7 - VLRLNHVGDWGTQF SYR_SYNY3 157 7 - VLRVNHIGDWGTQF SYR_CAEEL 280 3 - VLRLNHVGDWGTQF SYR_HUMAN 232 7 - VFKVNIINDRGVHI A71277 163 7 - VLRLNHVGDWGTQF SYR_CRILO 233 7 - VTRMNYLGDWGRQF SYRM_YEAST 219 7 - VIRANHVGDWGTQF SYR_HAEIN 153 7 - ITKINLINDRGVHI A70174 164 7 - VVREYYFNDHGAQI SYR_MYCTU 161 7 - VTREYYFNDHGRQI SYR_BRELA 161 7 - VTREYYFNDHGRQI SYR_CORGL 161 7 - VSREYYINDAGNQI SYR_BACSU 163 7 - VVREYYFNDHGAQV SYR_MYCLE 161 7 - VETHYYVNDMGRQM SYR_METJA 155 7 - VIRANHVGDWGTQF SYR_ECOLI 153 7 - Motif 4 width=22 Element Seqn Id St Int Rpt VVIKSDGKPAYIAGDLAYYLDK SYR_MYCLE 298 123 - IIQKKDGGYLYTTTDIACAKYR SYR_ECOLI 303 136 - VLIKEDKSYTYLAGDIVYHDEK SYR_HELPY 292 128 - VLVRQDNRPSYFGTDVAYHLDK SYR_MYCPN 288 130 - IVQKSDGGYNYATTDLAALNYR SYR_SYNY3 307 136 - ALLRSDGTTMYITQDIGTAIFR A71277 312 135 - VLIRSNGTSIYLTQDLGNIAVR A70174 319 141 - TVVKSDGGFTYDTSDLAALKYR SYR_CAEEL 424 130 - TIVKSDGGYTYDTSDLAAIKQR SYR_HUMAN 374 128 - TIVKSDGGFTYDTSDLAAIKQR SYR_CRILO 375 128 - VVQKSDGTTLYLTRDVGAAIER SYRM_YEAST 373 140 - IVQKKDGGFLYTTTDIAAAKYR SYR_HAEIN 303 136 - VVIKSDGKPAYIAGDLAYYLDK SYR_MYCTU 298 123 - VVIKSDGDAAYIAGDIAYVADK SYR_BRELA 298 123 - VVIKSDGDAAYIAGDIAYVADK SYR_CORGL 298 123 - VLIKKDGTYTYLLPDIAYHKDK SYR_BACSU 306 129 - VLARANGTSLYSTRDIAYHLDK SYR_METJA 304 135 -
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Final Motifs | Motif 1 width=16 Element Seqn Id St Int Rpt RIVVDFSSPNIAKEMH SYR_SYNY3 118 118 - RVLVDFSSPNIAKEMH SYR_CAEEL 245 245 - KVIVDFSSPNIAKEMH SYR_HUMAN 193 193 - KVIVDFSSPNIAKEMH SYR_CRILO 194 194 - KVVVEFSSPNIAKPFH SYRM_YEAST 180 180 - RAVVDFSSPNIAKEMH O23246 130 130 - RAVVDFSSPNIAKEMH O23247 182 182 - KVIIEFSSPNIAKPFH SYRC_YEAST 144 144 - KVIIDFSSPNIAKDMH O84460 115 115 - TVVIDYSSPNVAKEMH SYR_HAEIN 114 114 - RVILEHTSANPNGPLH SYR_METTH 114 114 - KVQLEYVSANPTGPLH O67068 113 113 - KVNLEFVSANPTGPIH SYR_MYCTU 122 122 - DVNLEFVSANPTGPIH SYR_BRELA 122 122 - DVNLEFVSANPTGPIH SYR_CORGL 122 122 - VAVIEFSSPNIAKPFH O74781 142 142 - RVQVEFVSANPTGDLH SYR_BACSU 124 124 - QINLEFVSANPTGPIH SYR_MYCLE 122 122 - KIILEHTSANPNGPLH SYR_METJA 116 116 - TIVVDYSAPNVAKEMH SYR_ECOLI 114 114 - KIFLEFVSANPTGPLH SYR_HELPY 111 111 - KVIVEHTSVNPTKPLH O59147 120 120 - EILIEHTSANPDGPLH SYR_ARCFU 105 105 - RIMVEFSSPNTNKPLH SYR_TREPA 124 124 - KIILEFSSPNTNKPLH SYR_BORBU 125 125 - KVLIEWVSANPTGELH SYR_MYCPN 105 105 - KILIESVSANPTGRIH SYR_MYCGE 105 105 - Motif 2 width=17 Element Seqn Id St Int Rpt HVGHLRSTIIGDCLARV SYR_SYNY3 133 -1 - HVGHLRSTIIGDSICRL SYR_CAEEL 260 -1 - HVGHLRSTIIGESISRL SYR_HUMAN 208 -1 - HVGHLRSTIIGESMSRL SYR_CRILO 209 -1 - HAGHLRSTIIGGFLSNL SYRM_YEAST 195 -1 - HVGHLRSTIIGDTLARM O23246 145 -1 - HVGHLRSTIIGDTLARM O23247 197 -1 - HAGHLRSTIIGGFLANL SYRC_YEAST 159 -1 - HVGHLRSTIIGDCLARC O84460 130 -1 - HVGHLRSTIIGDAVART SYR_HAEIN 129 -1 - HIGHIRNAIIGDSLARI SYR_METTH 129 -1 - HLGHGRGAVVGDTLARL O67068 128 -1 - HIGGTRWAAVGDALGRL SYR_MYCTU 137 -1 - HLGGTRWAAVGDSLGRV SYR_BRELA 137 -1 - HLGGTRWAAVGDSLGRV SYR_CORGL 137 -1 - HAGHLRSTIIGSFLANL O74781 157 -1 - HLGHARGAAVGDSLCNV SYR_BACSU 139 -1 - HIGGTRWAAVGDALGRL SYR_MYCLE 137 -1 - HIGHLRNAIIGDCLKRI SYR_METJA 131 -1 - HVGHLRSTIIGDAAVRT SYR_ECOLI 129 -1 - HIGHARGAVFGDSLAKI SYR_HELPY 126 -1 - HMGHARNAILGDVMARI O59147 135 -1 - HIGHIRNSIIGDTIARI SYR_ARCFU 120 -1 - HVGHLRNNAIGESLSRI SYR_TREPA 139 -1 - HVGHLRNDVIGESLSRI SYR_BORBU 140 -1 - HLGHVRNAFFGHVLNNL SYR_MYCPN 120 -1 - HLGHVRIAFFGDVLNNL SYR_MYCGE 120 -1 - Motif 3 width=14 Element Seqn Id St Int Rpt VLRLNHVGDWGTQF SYR_SYNY3 157 7 - VLRVNHIGDWGTQF SYR_CAEEL 280 3 - VLRLNHVGDWGTQF SYR_HUMAN 232 7 - VLRLNHVGDWGTQF SYR_CRILO 233 7 - VTRMNYLGDWGRQF SYRM_YEAST 219 7 - VLRRNHVGDWGTQF O23246 169 7 - VLRRNHVGDWGTQF O23247 221 7 - VIRMNYLGDWGKQF SYRC_YEAST 183 7 - VLRLNHIGDWGTAF O84460 154 7 - VIRANHVGDWGTQF SYR_HAEIN 153 7 - VETQYYVNDMGRQI SYR_METTH 153 7 - VTREYYINDAGRQV O67068 152 7 - VVREYYFNDHGAQI SYR_MYCTU 161 7 - VTREYYFNDHGRQI SYR_BRELA 161 7 - VTREYYFNDHGRQI SYR_CORGL 161 7 - VHRVNYLGDWGKQF O74781 181 7 - VSREYYINDAGNQI SYR_BACSU 163 7 - VVREYYFNDHGAQV SYR_MYCLE 161 7 - VETHYYVNDMGRQM SYR_METJA 155 7 - VIRANHVGDWGTQF SYR_ECOLI 153 7 - VLCEYYVNDMGSQI SYR_HELPY 150 7 - VEVQNYIDDLGIQF O59147 159 7 - VKTHYYVNDMGRQT SYR_ARCFU 144 7 - VFKVNIINDRGVHI SYR_TREPA 163 7 - ITKINLINDRGVHI SYR_BORBU 164 7 - TVREYWVNDYGQQA SYR_MYCPN 144 7 - TVCEYWVNDYGQQA SYR_MYCGE 144 7 - Motif 4 width=22 Element Seqn Id St Int Rpt IVQKSDGGYNYATTDLAALNYR SYR_SYNY3 307 136 - TVVKSDGGFTYDTSDLAALKYR SYR_CAEEL 424 130 - TIVKSDGGYTYDTSDLAAIKQR SYR_HUMAN 374 128 - TIVKSDGGFTYDTSDLAAIKQR SYR_CRILO 375 128 - VVQKSDGTTLYLTRDVGAAIER SYRM_YEAST 373 140 - IVVKSDGGFNYASTDLTALWYR O23246 312 129 - MVVKSDGGFNYASTDLTALWYR O23247 364 129 - IVQKSDGTTLYLTRDVGAAMDR SYRC_YEAST 337 140 - MIQKSDGGYNYATTDVAAMRYR O84460 293 125 - IVQKKDGGFLYTTTDIAAAKYR SYR_HAEIN 303 136 - VLTRSDGTSLYSTRDIAYHLQK SYR_METTH 299 132 - VVKRSDGTYTYFASDIAYHYNK O67068 330 164 - VVIKSDGKPAYIAGDLAYYLDK SYR_MYCTU 298 123 - VVIKSDGDAAYIAGDIAYVADK SYR_BRELA 298 123 - VVIKSDGDAAYIAGDIAYVADK SYR_CORGL 298 123 - IVQKRDGTTLYLTRDIGTAYKR O74781 349 154 - VLIKKDGTYTYLLPDIAYHKDK SYR_BACSU 306 129 - VVIKSDGKPAYIAGDLAYYLDK SYR_MYCLE 298 123 - VLARANGTSLYSTRDIAYHLDK SYR_METJA 304 135 - IIQKKDGGYLYTTTDIACAKYR SYR_ECOLI 303 136 - VLIKEDKSYTYLAGDIVYHDEK SYR_HELPY 292 128 - VLRRSDGTATYTGKDIAYHLWK O59147 321 148 - VLRRENGTTLYITRDLAYHMWK SYR_ARCFU 285 127 - ALLRSDGTTMYITQDIGTAIFR SYR_TREPA 312 135 - VLIRSNGTSIYLTQDLGNIAVR SYR_BORBU 319 141 - VLVRQDNRPSYFGTDVAYHLDK SYR_MYCPN 288 130 - VLIRSDKRASYFGTDVAYHLEK SYR_MYCGE 288 130 -
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