Identifier | TRNASYNTHVAL  [View Relations]  [View Alignment]  
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Accession | PR00986 |
No. of Motifs | 5 |
Creation Date | 17-SEP-1998  (UPDATE 07-JUN-1999) |
Title | Valyl-tRNA synthetase signature |
Database References | PRINTS; PR90000 TRNASYNTH; PR90001 TRNASYNTHCLI PROSITE; PS00178 AA_TRNA_LIGASE_I BLOCKS; BL00178 PFAM; PF00749 TRNA-SYNT_1 INTERPRO; IPR002303 |
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.
Valyl-tRNA synthetase (EC 6.1.1.9 ) is specific to valine and belongs to
class I.
TRNASYNTHVAL is a 5-element fingerprint that provides a signature for
valyl-tRNA synthetases. The fingerprint was derived from an initial
alignment of 9 sequences: the motifs were drawn from conserved regions
within the C-terminal portion of the alignment - motif 1 includes part
of the region encoded by PROSITE pattern AA_TRNA_LIGASE_I (PS00178). Two
iterations on OWL30.2 were required to reach convergence, at which point a
true set comprising 26 sequences was identified. Several partial matches
were also found: three of these are valine AATRSs from Plasmodium sp. that
fail to make significant matches with a number of motifs; three are
fragments; and the remaining matches are closely related isoleucine AATRSs
from Methanobacterium.
An update on SPTR37_9f identified a true set of 27 sequences, and 3
partial matches.
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Summary Information | 27 codes involving 5 elements 1 codes involving 4 elements 2 codes involving 3 elements 0 codes involving 2 elements
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Composite Feature Index | 5 | 27 | 27 | 27 | 27 | 27 | 4 | 0 | 1 | 1 | 1 | 1 | 3 | 2 | 0 | 0 | 2 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | | 1 | 2 | 3 | 4 | 5 |
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True Positives | O14160 O53175 O58052 O67411 O75005 O77443 O84304 SYV_ARATH SYV_ARCFU SYV_BACST SYV_BACSU SYV_BORBU SYV_ECOLI SYV_FUGRU SYV_HAEIN SYV_HELPY SYV_HUMAN SYV_LACCA SYV_METJA SYV_METTH SYV_MYCGE SYV_MYCPN SYV_NEUCR SYV_SYNY3 SYV_THETH SYV_TREPA SYV_YEAST |
True Positive Partials | |
Sequence Titles | O14160 PUTATIVE VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). O53175 VALYL-TRNA SYNTHETASE - MYCOBACTERIUM TUBERCULOSIS. O58052 896AA LONG HYPOTHETICAL VALYL-TRNA SYNTHETASE - PYROCOCCUS HORIKOSHII. O67411 VALYL-TRNA SYNTHETASE - AQUIFEX AEOLICUS. O75005 VALYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). O77443 VALYL TRNA SYNTHETASE - GIARDIA INTESTINALIS. O84304 VALYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS. SYV_ARATH VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). SYV_ARCFU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - ARCHAEOGLOBUS FULGIDUS. SYV_BACST VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - BACILLUS STEAROTHERMOPHILUS. SYV_BACSU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - BACILLUS SUBTILIS. SYV_BORBU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE). SYV_ECOLI VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - ESCHERICHIA COLI. SYV_FUGRU VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES). SYV_HAEIN VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - HAEMOPHILUS INFLUENZAE. SYV_HELPY VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI). SYV_HUMAN VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - HOMO SAPIENS (HUMAN). SYV_LACCA VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - LACTOBACILLUS CASEI. SYV_METJA VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - METHANOCOCCUS JANNASCHII. SYV_METTH VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - METHANOBACTERIUM THERMOAUTOTROPHICUM. SYV_MYCGE VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - MYCOPLASMA GENITALIUM. SYV_MYCPN VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - MYCOPLASMA PNEUMONIAE. SYV_NEUCR VALYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - NEUROSPORA CRASSA. SYV_SYNY3 VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803). SYV_THETH VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS). SYV_TREPA VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - TREPONEMA PALLIDUM. SYV_YEAST VALYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). Q23360 SIMILARITY TO THE CARBOXYL TWO-THIRDS OF VALYL-TRNA SYNTHETASES - CAENORHABDITIS ELEGANS. Q26177 GAM1 GENE - PLASMODIUM VIVAX. Q26178 GAM1 GENE - PLASMODIUM VIVAX.
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Scan History | OWL30_2 2 50 NSINGLE SPTR37_9f 2 33 NSINGLE
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Initial Motifs | Motif 1 width=12 Element Seqn Id St Int Rpt FTIVIPPPNVTG SYV_BACST 42 42 - YSVVIPPPNVTG SYV_BACSU 42 42 - FCIPAPPPNVTG SYV_YEAST 183 183 - FMMCIPPPNVTG SYV_HUMAN 337 337 - YCVVIPPPNVTG SYV_SYNY3 39 39 - FMMCIPPPNVTG SYV_FUGRU 286 286 - FCLMMPPPNVTG SYV_HELPY 44 44 - FVIFMPPPNVTG SYV_THETH 36 36 - YIIDTPPPYPTG SYV_METJA 36 36 - Motif 2 width=18 Element Seqn Id St Int Rpt HPDDERYKHLIGKMVKLP SYV_BACST 236 182 - HPEDERYKHLIGKTVILP SYV_BACSU 236 182 - HPDDDRYKHLHGKFIQHP SYV_YEAST 394 199 - HPKDTRYQHLKGKNVIHP SYV_HUMAN 550 201 - NPHDERYAAMVGKTITLP SYV_SYNY3 233 182 - HPSDSRYQHLKGKTVLHP SYV_FUGRU 497 199 - NPNDERYKHLVGQKAILP SYV_HELPY 237 181 - HPEDERYRHLLGKRARIP SYV_THETH 228 180 - HPEDERYKHLIGKEFIVP SYV_METJA 227 179 - Motif 3 width=14 Element Seqn Id St Int Rpt RSGAVIEPYLSTQW SYV_BACST 351 97 - RSGAVVEPYLSTQW SYV_BACSU 351 97 - RSGDIIEPLLKPQW SYV_YEAST 511 99 - RSKDVVEPLLRPQW SYV_HUMAN 665 97 - RGKVPVEPLLSTQW SYV_SYNY3 348 97 - RSKDIVEPLMKPQW SYV_FUGRU 612 97 - RCHNVVEPYVSKQW SYV_HELPY 352 97 - RCGTPIEYAIFPQW SYV_THETH 338 92 - RCKTPIEIIVTEQW SYV_METJA 342 97 - Motif 4 width=22 Element Seqn Id St Int Rpt DPDVLDTWFSSALWPFSTMGWP SYV_BACST 445 80 - DTDVLDTWFSSALWPFSTMGWP SYV_BACSU 445 80 - DEDVLDTWFSSGLWPFSTLGWP SYV_YEAST 624 99 - DEDVLDTWFSSGLFPLSILGWP SYV_HUMAN 783 104 - DPDVLDTWFSSGLWPFSTMGWP SYV_SYNY3 460 98 - DEDVLDTWFSSGINPFSILGWP SYV_FUGRU 730 104 - DKDVLDTWFSSGLWAFSTLGWG SYV_HELPY 448 82 - DEDVFDTWFSSALWPLSTLGWP SYV_THETH 441 89 - ETDVLDTWMDSSITPMVITKWL SYV_METJA 448 92 - Motif 5 width=19 Element Seqn Id St Int Rpt YPTDVLVTGYDIIFFWVSR SYV_BACST 477 10 - YPTDVLVTGYDIIFFWVSR SYV_BACSU 477 10 - YPFSMLETGWDILFFWVTR SYV_YEAST 655 9 - YPGTLLETGHDILFFWVAR SYV_HUMAN 814 9 - YPTSTLVTGFDIIFFWVAR SYV_SYNY3 491 9 - YPGTLLETGHDILFFWVAR SYV_FUGRU 761 9 - YPNTTLITGFDILFFWVAR SYV_HELPY 485 15 - YPGDVLVTGYDILFLWVSR SYV_THETH 472 9 - YPVQLRPQGHDIIRTWAFY SYV_METJA 479 9 -
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Final Motifs | Motif 1 width=12 Element Seqn Id St Int Rpt FTIVIPPPNVTG SYV_BACST 42 42 - YSVVIPPPNVTG SYV_BACSU 42 42 - YSIVLPPPNVTG O53175 36 36 - FVIVLPPPNVTG SYV_ARATH 170 170 - FCIPAPPPNVTG SYV_YEAST 183 183 - YCIAIPPPNVTG SYV_HAEIN 41 41 - FSMVAPPPNVTG SYV_BORBU 38 38 - FSVVIPPPNVTG O67411 36 36 - FMMCIPPPNVTG SYV_HUMAN 337 337 - YSIVMPPPNVTG O84304 40 40 - FCIMIPPPNVTG SYV_ECOLI 35 35 - YCVVIPPPNVTG SYV_SYNY3 39 39 - FMMCIPPPNVTG SYV_FUGRU 286 286 - FVIAIPPPNITG SYV_TREPA 62 62 - FVITSPPPNVTG O75005 132 132 - YSIVIPPPNVTG SYV_LACCA 61 61 - FCLMMPPPNVTG SYV_HELPY 44 44 - FVIFMPPPNVTG SYV_THETH 36 36 - FVIPLPPPNVTG SYV_NEUCR 172 172 - FTLLIPPPNVTG O77443 97 97 - FPILLPPPNITG O14160 2 2 - FTAILPPPNLTG SYV_MYCGE 39 39 - FTAILPPPNLTG SYV_MYCPN 39 39 - YIIDTPPPYPTG SYV_ARCFU 36 36 - YIIDTPPPYPTG SYV_METJA 36 36 - YIIDTPPPYPTG SYV_METTH 59 59 - YAIDTPPPFTSG O58052 41 41 - Motif 2 width=18 Element Seqn Id St Int Rpt HPDDERYKHLIGKMVKLP SYV_BACST 236 182 - HPEDERYKHLIGKTVILP SYV_BACSU 236 182 - HPDDERYRHLVGTSLAHP O53175 231 183 - HPDDARYKHLHGKFAVHP SYV_ARATH 380 198 - HPDDDRYKHLHGKFIQHP SYV_YEAST 394 199 - HPEDERYQSLIGKTVVLP SYV_HAEIN 242 189 - NPNDERYKSLVGKEVTIP SYV_BORBU 231 181 - NPNDDRYKHLVGKRARLP O67411 235 187 - HPKDTRYQHLKGKNVIHP SYV_HUMAN 550 201 - SPEDLRYSHLIGAKVVVP O84304 235 183 - NPEDPRYKDLIGKYVILP SYV_ECOLI 236 189 - NPHDERYAAMVGKTITLP SYV_SYNY3 233 182 - HPSDSRYQHLKGKTVLHP SYV_FUGRU 497 199 - HPDDARYQSLIGRKVCVP SYV_TREPA 273 199 - HPQDPRYKHLHGKFVKHP O75005 343 199 - HPGDERYKDMVGTELILP SYV_LACCA 255 182 - NPNDERYKHLVGQKAILP SYV_HELPY 237 181 - HPEDERYRHLLGKRARIP SYV_THETH 228 180 - NPEDPRYTHLVGKFARHP SYV_NEUCR 383 199 - HPRDHRYTDLHGRCLFHP O77443 377 268 - SPHDERYKKYVGRFVKHP O14160 211 197 - NPKDKRYTNFWNKLVVNP SYV_MYCGE 234 183 - HPKDKHYHSFVKQKVVNP SYV_MYCPN 234 183 - HPDDERNKHLIGKKVRVP SYV_ARCFU 222 174 - HPEDERYKHLIGKEFIVP SYV_METJA 227 179 - HPDDERFREFEDKLIEVP SYV_METTH 250 179 - HPDDERYKHLVGKKVKLP O58052 230 177 - Motif 3 width=14 Element Seqn Id St Int Rpt RSGAVIEPYLSTQW SYV_BACST 351 97 - RSGAVVEPYLSTQW SYV_BACSU 351 97 - RSGEPIEPRLSLQW O53175 347 98 - RTNDVIEPMIKPQW SYV_ARATH 497 99 - RSGDIIEPLLKPQW SYV_YEAST 511 99 - RGGVPIEPMLTDQW SYV_HAEIN 375 115 - RSGEVIEPYLSTQW SYV_BORBU 347 98 - RCKTVIEPMVSVQW O67411 362 109 - RSKDVVEPLLRPQW SYV_HUMAN 665 97 - RSGAIIEPYLSKQW O84304 350 97 - RGGVVIEPMLTDQW SYV_ECOLI 369 115 - RGKVPVEPLLSTQW SYV_SYNY3 348 97 - RSKDIVEPLMKPQW SYV_FUGRU 612 97 - RCEAVIEPYLSLQW SYV_TREPA 389 98 - KTSDIIEPVMKPQW O75005 459 98 - RTGVQVEARLSTQW SYV_LACCA 370 97 - RCHNVVEPYVSKQW SYV_HELPY 352 97 - RCGTPIEYAIFPQW SYV_THETH 338 92 - KSKDVIEPMMTEQW SYV_NEUCR 498 97 - RSGDILEPMVKPQW O77443 506 111 - RTGDVIEPVMVPQW O14160 327 98 - RSGTVVEPMLSKQW SYV_MYCGE 349 97 - RSDTVVEPLLSKQW SYV_MYCPN 349 97 - RCKTPVEIIPAEQW SYV_ARCFU 337 97 - RCKTPIEIIVTEQW SYV_METJA 342 97 - RCKTPIEILVKKQW SYV_METTH 365 97 - SCMAPIELLPKKQW O58052 348 100 - Motif 4 width=22 Element Seqn Id St Int Rpt DPDVLDTWFSSALWPFSTMGWP SYV_BACST 445 80 - DTDVLDTWFSSALWPFSTMGWP SYV_BACSU 445 80 - DPDVLDTWFSSALWPFSTLGWP O53175 439 78 - DPDVLDTWFSSGLFPLSVLGWP SYV_ARATH 615 104 - DEDVLDTWFSSGLWPFSTLGWP SYV_YEAST 624 99 - DEDVLDTWFSSGLWTFSTLGWP SYV_HAEIN 475 86 - DPDVLDTWFSSWLWPFSSLGWP SYV_BORBU 445 84 - ERDVLDTWFSSALWPFGVFGWP O67411 721 345 - DEDVLDTWFSSGLFPLSILGWP SYV_HUMAN 783 104 - DPDVLDTWFSSGLWPLTCFGWP O84304 449 85 - DEDVLDTWFSSALWTFSTLGWP SYV_ECOLI 469 86 - DPDVLDTWFSSGLWPFSTMGWP SYV_SYNY3 460 98 - DEDVLDTWFSSGINPFSILGWP SYV_FUGRU 730 104 - DPDVLDTWFSSWLWPFSTLGWP SYV_TREPA 487 84 - DEDVLDTWFSSGLWPFSTLGWP O75005 573 100 - DPDVLDTWFSSALWPFSTMGWP SYV_LACCA 465 81 - DKDVLDTWFSSGLWAFSTLGWG SYV_HELPY 448 82 - DEDVFDTWFSSALWPLSTLGWP SYV_THETH 441 89 - DPDCLDTWFSSGLWPMAILGWP SYV_NEUCR 612 100 - DDDVTDTWFSSGLFPFSCFADS O77443 627 107 - DSDVLDTWFSSALLPLSAFGWP O14160 423 82 - SKDVLDTWFSSSLWPLICLNWE SYV_MYCGE 439 76 - STDVLDTWFSSSLWPLICLDWH SYV_MYCPN 439 76 - ETDVLDTWMDSSITPLMICGWP SYV_ARCFU 443 92 - ETDVLDTWMDSSITPMVITKWL SYV_METJA 448 92 - EEDVLDTWMDSSISPLSVAGWP SYV_METTH 472 93 - VTDVLDCWVDSSITPLIITKWH O58052 455 93 - Motif 5 width=19 Element Seqn Id St Int Rpt YPTDVLVTGYDIIFFWVSR SYV_BACST 477 10 - YPTDVLVTGYDIIFFWVSR SYV_BACSU 477 10 - YPTSVLVTGYDILFFWVAR O53175 470 9 - YPTSVLETGHDILFFWVAR SYV_ARATH 646 9 - YPFSMLETGWDILFFWVTR SYV_YEAST 655 9 - HPTDVLITGFDIIFFWVAR SYV_HAEIN 506 9 - YPTNTLITAYDIIFFWVAR SYV_BORBU 476 9 - YPTDLLVTGFDIIFFWVAR O67411 752 9 - YPGTLLETGHDILFFWVAR SYV_HUMAN 814 9 - YPTAVLVTGHDILFFWVTR O84304 481 10 - HPTSVMVSGFDIIFFWIAR SYV_ECOLI 500 9 - YPTSTLVTGFDIIFFWVAR SYV_SYNY3 491 9 - YPGTLLETGHDILFFWVAR SYV_FUGRU 761 9 - YPTSAVITAYDIIFFWVAR SYV_TREPA 518 9 - YPTTLMETGWDILFFWIAR O75005 604 9 - YPTDTLVTGYDIIPFWVAR SYV_LACCA 497 10 - YPNTTLITGFDILFFWVAR SYV_HELPY 485 15 - YPGDVLVTGYDILFLWVSR SYV_THETH 472 9 - FPTSMLETGWDILFFWVSR SYV_NEUCR 644 10 - YPGSVLETGNDIIFFWVAR O77443 656 7 - QPLPFIESGQDILFFWIAR O14160 450 5 - HETELLVTGYDILFFWVLR SYV_MYCGE 466 5 - VPTDLLVTGYDILFFWVLR SYV_MYCPN 466 5 - YPTHLRPQGHDIIRTWAFY SYV_ARCFU 469 4 - YPVQLRPQGHDIIRTWAFY SYV_METJA 479 9 - FPADLRPQGHDIIRTWAFY SYV_METTH 501 7 - FPTALRPQGTDIIRTWAFY O58052 493 16 -
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