| 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
BLOCKS; BL00179
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 | |
| 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 -
|