| Identifier | TRNASYNTHVAL [View Relations] [View Alignment]
|
| 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).
|
| 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.
|
| Summary Information | 27 codes involving 5 elements
1 codes involving 4 elements
2 codes involving 3 elements
0 codes involving 2 elements
|
| 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 |
|
| 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.
|
| Scan History | OWL30_2 2 50 NSINGLE
SPTR37_9f 2 33 NSINGLE
|
| 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 -
|
| 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 -
|