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PR01038

Identifier
TRNASYNTHARG  [View Relations]  [View Alignment]  
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
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).

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.
Summary Information
  27 codes involving  4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
427272727
30000
20011
1234
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
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.
Scan History
OWL31_1    2  100  NSINGLE    
SPTR37_9f 2 30 NSINGLE
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 -
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 -