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PR01046

Identifier
TRNASYNTHPRO  [View Relations]  [View Alignment]  
Accession
PR01046
No. of Motifs
4
Creation Date
17-DEC-1998  (UPDATE 07-JUN-1999)
Title
Prolyl-tRNA synthetase signature
Database References
PRINTS; PR90000 TRNASYNTH; PR90002 TRNASYNTHCLII
PROSITE; PS00179 AA_TRNA_LIGASE_II_1; PS00339 AA_TRNA_LIGASE_II_2
INTERPRO; IPR002316
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.
     
Prolyl-tRNA synthetase (EC 6.1.1.5) is specific to proline and belongs to 
class II.
 
TRNASYNTHPRO is a 4-element fingerprint that provides a signature for 
prolyl-tRNA synthetases. The fingerprint was derived from an initial
alignment of 14 sequences: the motifs were drawn from short conserved 
regions towards the N-terminal portion of the alignment (note that the
prolyl-tRNA synthetase lies in the C-terminal domain of the multifunctional
proteins SYEP_DROME and SYEP_HUMAN, which also contain N-terminal glutamyl-
tRNA synthetases) - motifs 3 and 4 overlap the region encoded by PROSITE
pattern AA_TRNA_LIGASE_II_1 (PS00179). Two iterations on OWL31.1 were 
required to reach convergence, at which point a true set comprising 29 
sequences was identified. Several partial matches were also found, all of
which are glycyl-tRNA synthetases that match motifs 3 and 4.
 
An update on SPTR37_9f identified a true set of 27 sequences.
Summary Information
27 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
427272727
30000
20000
1234
True Positives
O31755        O45869        O51363        O58734        
O60155 O66690 O74765 O84398
Q22620 SYEP_DROME SYEP_HUMAN SYPC_CANAL
SYPC_YEAST SYP_ARCFU SYP_CHLTR SYP_ECOLI
SYP_HAEIN SYP_HELPY SYP_METJA SYP_METTH
SYP_MYCGE SYP_MYCPN SYP_MYCTU SYP_SYNY3
SYP_TREPA SYP_ZYMMO YHI0_YEAST
Sequence Titles
O31755      PROLYL-TRNA SYNTHETASE - BACILLUS SUBTILIS.   
O45869 T27F6.5 PROTEIN - CAENORHABDITIS ELEGANS.
O51363 PROLYL-TRNA SYNTHETASE (PROS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O58734 480AA LONG HYPOTHETICAL PROLYL-TRNA SYNTHETASE - PYROCOCCUS HORIKOSHII.
O60155 PUTATIVE PROLYL-TRNA SYNTHETASE - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O66690 PROLINE-TRNA SYNTHETASE - AQUIFEX AEOLICUS.
O74765 PUTATIVE PROLINE-TRNA SYNTHETASE - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O84398 PROLYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
Q22620 SIMILAR TO MULTIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE - CAENORHABDITIS ELEGANS.
SYEP_DROME MULTIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE [INCLUDES: GLUTAMYL-TRNA SYNTHETASE (EC 6.1.1.17) (GLUTAMATE--TRNA LIGASE); PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE)] - DROSOPHILA MELANOGASTER (FRUIT FLY).
SYEP_HUMAN MULTIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE [INCLUDES: GLUTAMYL-TRNA SYNTHETASE (EC 6.1.1.17) (GLUTAMATE--TRNA LIGASE); PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE)] - HOMO SAPIENS (HUMAN).
SYPC_CANAL PROLYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.15) (PROLINE-- TRNA LIGASE) (PRORS) - CANDIDA ALBICANS (YEAST).
SYPC_YEAST PROBABLE PROLYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.15) (PROLINE-- TRNA LIGASE) (PRORS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
SYP_ARCFU PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - ARCHAEOGLOBUS FULGIDUS.
SYP_CHLTR PROBABLE PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - CHLAMYDIA TRACHOMATIS.
SYP_ECOLI PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) (GLOBAL RNA SYNTHESIS FACTOR) - ESCHERICHIA COLI.
SYP_HAEIN PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - HAEMOPHILUS INFLUENZAE.
SYP_HELPY PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYP_METJA PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - METHANOCOCCUS JANNASCHII.
SYP_METTH PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
SYP_MYCGE PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - MYCOPLASMA GENITALIUM.
SYP_MYCPN PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - MYCOPLASMA PNEUMONIAE.
SYP_MYCTU PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - MYCOBACTERIUM TUBERCULOSIS.
SYP_SYNY3 PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
SYP_TREPA PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - TREPONEMA PALLIDUM.
SYP_ZYMMO PUTATIVE PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - ZYMOMONAS MOBILIS.
YHI0_YEAST PUTATIVE PROLYL-TRNA SYNTHETASE YHR020W (EC 6.1.1.15) (PROLINE--TRNA LIGASE) (PRORS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
Scan History
OWL31_1    2  50   NSINGLE    
SPTR37_9f 2 36 NSINGLE
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
ECLLPQLQPSELWKMSGRW SYP_SYNY3 82 82 -
EVLMPVVQPAELWEESGRW SYP_HAEIN 68 68 -
EVSMPVVQPADLWQESGRW SYP_ECOLI 68 68 -
EVCLPLLQPAELWEKTGRW SYP_CHLTR 68 68 -
NILMSFVVLASLWEKSGRL SYP_HELPY 68 68 -
EILFPALLPRAPYETTNRW SYP_MYCTU 70 70 -
EVYFPALIPETELGKEGEH SYP_ARCFU 164 164 -
EALFPMLIPEDLLAKEAEH SYP_METJA 55 55 -
ELLMPTLQTADLWPESGRY SYP_ZYMMO 68 68 -
EVLFPLLVPEDELAKEAIH SYP_METTH 71 71 -
EVSLSLISHKELWKLTNRW SYPC_CANAL 78 78 -
EVSLSAISSKALWQATDRW SYPC_YEAST 76 76 -
QVQLPTLSFYSEYQKEKRH SYP_MYCPN 78 78 -
QVQLPTLSFYSEYQKEKTH SYP_MYCGE 78 78 -

Motif 2 width=12
Element Seqn Id St Int Rpt
LGLGPTHEEVIT SYP_SYNY3 121 20 -
FVLGPTHEEVIT SYP_HAEIN 104 17 -
FVLGPTHEEVIT SYP_ECOLI 104 17 -
MCLAPTHEEVVS SYP_CHLTR 106 19 -
FVLSPTLEENIT SYP_HELPY 104 17 -
YLLGPTHEELFT SYP_MYCTU 106 17 -
LALRPTSETAMY SYP_ARCFU 205 22 -
LALRPTSETPIY SYP_METJA 96 22 -
LLYGPTNEEMIT SYP_ZYMMO 104 17 -
LALRPTSETVMY SYP_METTH 112 22 -
YLLVPTAEEEIT SYPC_CANAL 109 12 -
YCLTATCEEDIT SYPC_YEAST 110 15 -
LVLRPTSEIAFC SYP_MYCPN 119 22 -
LVLRPTSEIAFC SYP_MYCGE 119 22 -

Motif 3 width=9
Element Seqn Id St Int Rpt
QIQTKFRDE SYP_SYNY3 151 18 -
QIQTKFRDE SYP_HAEIN 134 18 -
QIQTKFRDE SYP_ECOLI 134 18 -
QIGTKFRDE SYP_CHLTR 136 18 -
QIHTKFRDE SYP_HELPY 134 18 -
QIQTKYRDE SYP_MYCTU 136 18 -
QIVNTFRYE SYP_ARCFU 235 18 -
QIVNTFRYE SYP_METJA 126 18 -
HIQWKFRDE SYP_ZYMMO 134 18 -
QVVNTFRYE SYP_METTH 142 18 -
QINPKFRNE SYPC_CANAL 140 19 -
QMTRKYRDE SYPC_YEAST 140 18 -
QWTCVFRAE SYP_MYCPN 149 18 -
QWTQVFRAE SYP_MYCGE 149 18 -

Motif 4 width=12
Element Seqn Id St Int Rpt
RPRFGLMRGREF SYP_SYNY3 161 1 -
RPRFGVMRSREF SYP_HAEIN 144 1 -
RPRFGVMRSREF SYP_ECOLI 144 1 -
RPRFGLMRAKEF SYP_CHLTR 146 1 -
RPRFGLVRAREF SYP_HELPY 144 1 -
RPRAGILRAREF SYP_MYCTU 146 1 -
KHTRPLIRLREI SYP_ARCFU 245 1 -
KHTRPLIRLREI SYP_METJA 136 1 -
RPRFGVMRGREF SYP_ZYMMO 144 1 -
KHTRPLIRVREI SYP_METTH 152 1 -
RPRGGLLRGKEF SYPC_CANAL 150 1 -
RPRGGILRGREF SYPC_YEAST 150 1 -
KNTRPFLRNSEF SYP_MYCPN 158 0 -
KNTRPFLRNSEF SYP_MYCGE 158 0 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
ECLLPQLQPSELWKMSGRW SYP_SYNY3 82 82 -
EVLMPVVQPAELWEESGRW SYP_HAEIN 68 68 -
EVSMPVVQPADLWQESGRW SYP_ECOLI 68 68 -
EVCLPLLQPAELWEKTGRW O84398 68 68 -
EVCLPLLQPAELWEKTGRW SYP_CHLTR 68 68 -
ELLLTVLNPKELWEETGRW O66690 68 68 -
EMLMPALQQAETWQESGRW O31755 68 68 -
AISLAHLSSKEIWEKSGRW O74765 73 73 -
NILMSFVVLASLWEKSGRL SYP_HELPY 68 68 -
EILFPALLPRAPYETTNRW SYP_MYCTU 70 70 -
EVYFPALIPETELGKEGEH SYP_ARCFU 164 164 -
EALFPMLIPEDLLAKEAEH SYP_METJA 55 55 -
ECTAPVVTPAELWKESGRW SYP_TREPA 66 66 -
ELLMPTLQTADLWPESGRY SYP_ZYMMO 68 68 -
EVLFPLLVPEDELAKEAIH SYP_METTH 71 71 -
EVSLSLISHKELWKLTNRW SYPC_CANAL 78 78 -
EVLFPALIPETEFKKEAEH O58734 63 63 -
KIAMPIVGTQQLWEKTGRW O45869 68 68 -
ECYFPIFVSKAVLEKEKTH SYEP_DROME 1275 1275 -
NCYFPMFVSQSALEKEKTH SYEP_HUMAN 1003 1003 -
NAYFPMFVSSRVLEKEKDH YHI0_YEAST 246 246 -
NGYFPLFVSSKVLEKEKDH O60155 266 266 -
NCYFPMFVSNAALEREKTH Q22620 150 150 -
NAYFPMLIPYSFLEREKDH O51363 63 63 -
EVSLSAISSKALWQATDRW SYPC_YEAST 76 76 -
QVQLPTLSFYSEYQKEKRH SYP_MYCPN 78 78 -
QVQLPTLSFYSEYQKEKTH SYP_MYCGE 78 78 -

Motif 2 width=12
Element Seqn Id St Int Rpt
LGLGPTHEEVIT SYP_SYNY3 121 20 -
FVLGPTHEEVIT SYP_HAEIN 104 17 -
FVLGPTHEEVIT SYP_ECOLI 104 17 -
MCLAPTHEEVVS O84398 106 19 -
MCLAPTHEEVVS SYP_CHLTR 106 19 -
YCLGPTHEEEIT O66690 104 17 -
FALGATHEEVIT O31755 104 17 -
MCLAPTHEEDVT O74765 109 17 -
FVLSPTLEENIT SYP_HELPY 104 17 -
YLLGPTHEELFT SYP_MYCTU 106 17 -
LALRPTSETAMY SYP_ARCFU 205 22 -
LALRPTSETPIY SYP_METJA 96 22 -
LLFSPTAEESFT SYP_TREPA 102 17 -
LLYGPTNEEMIT SYP_ZYMMO 104 17 -
LALRPTSETVMY SYP_METTH 112 22 -
YLLVPTAEEEIT SYPC_CANAL 109 12 -
LVLRPTSETAMY O58734 104 22 -
MCLQPTAEEMCT O45869 104 17 -
IAVRPTSETVMY SYEP_DROME 1316 22 -
IAIRPTSETVMY SYEP_HUMAN 1044 22 -
IAIRPTSETVMY YHI0_YEAST 287 22 -
IAIRPTSETVMY O60155 307 22 -
IAIRPTSETVMY Q22620 191 22 -
LVLRPTSETIIW O51363 104 22 -
YCLTATCEEDIT SYPC_YEAST 110 15 -
LVLRPTSEIAFC SYP_MYCPN 119 22 -
LVLRPTSEIAFC SYP_MYCGE 119 22 -

Motif 3 width=9
Element Seqn Id St Int Rpt
QIQTKFRDE SYP_SYNY3 151 18 -
QIQTKFRDE SYP_HAEIN 134 18 -
QIQTKFRDE SYP_ECOLI 134 18 -
QIGTKFRDE O84398 136 18 -
QIGTKFRDE SYP_CHLTR 136 18 -
QIQVKFRDE O66690 134 18 -
QIQSKFRDE O31755 134 18 -
QIGRKFRDE O74765 139 18 -
QIHTKFRDE SYP_HELPY 134 18 -
QIQTKYRDE SYP_MYCTU 136 18 -
QIVNTFRYE SYP_ARCFU 235 18 -
QIVNTFRYE SYP_METJA 126 18 -
QINAKYRDE SYP_TREPA 132 18 -
HIQWKFRDE SYP_ZYMMO 134 18 -
QVVNTFRYE SYP_METTH 142 18 -
QINPKFRNE SYPC_CANAL 140 19 -
QIVNVYRYE O58734 134 18 -
QIGEKFRDE O45869 135 19 -
QWNNVVRWE SYEP_DROME 1346 18 -
QWCNVVRWE SYEP_HUMAN 1074 18 -
QWNSVVRWE YHI0_YEAST 317 18 -
QWNSVVRWE O60155 337 18 -
QWCNVVRWE Q22620 221 18 -
QWANVVRWE O51363 134 18 -
QMTRKYRDE SYPC_YEAST 140 18 -
QWTCVFRAE SYP_MYCPN 149 18 -
QWTQVFRAE SYP_MYCGE 149 18 -

Motif 4 width=12
Element Seqn Id St Int Rpt
RPRFGLMRGREF SYP_SYNY3 161 1 -
RPRFGVMRSREF SYP_HAEIN 144 1 -
RPRFGVMRSREF SYP_ECOLI 144 1 -
RPRFGLMRAKEF O84398 146 1 -
RPRFGLMRAKEF SYP_CHLTR 146 1 -
RPRFGLIRAREF O66690 144 1 -
RPRFGLLRGREF O31755 144 1 -
RPRGGLLRGREF O74765 149 1 -
RPRFGLVRAREF SYP_HELPY 144 1 -
RPRAGILRAREF SYP_MYCTU 146 1 -
KHTRPLIRLREI SYP_ARCFU 245 1 -
KHTRPLIRLREI SYP_METJA 136 1 -
RPRYGLMRAREF SYP_TREPA 142 1 -
RPRFGVMRGREF SYP_ZYMMO 144 1 -
KHTRPLIRVREI SYP_METTH 152 1 -
RPRGGLLRGKEF SYPC_CANAL 150 1 -
KHTRPLIRVREI O58734 144 1 -
NPRFGLMRGRQF O45869 145 1 -
KQPTPFLRTREF SYEP_DROME 1356 1 -
KHPQPFLRTREF SYEP_HUMAN 1084 1 -
KHPQPFLRTREF YHI0_YEAST 327 1 -
KNPQPFLRTREF O60155 347 1 -
KHPTPFLRTREF Q22620 231 1 -
KRTRPFLRTTEF O51363 143 0 -
RPRGGILRGREF SYPC_YEAST 150 1 -
KNTRPFLRNSEF SYP_MYCPN 158 0 -
KNTRPFLRNSEF SYP_MYCGE 158 0 -