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PR00983

Identifier
TRNASYNTHCYS  [View Relations]  [View Alignment]  
Accession
PR00983
No. of Motifs
4
Creation Date
16-SEP-1998  (UPDATE 07-JUN-1999)
Title
Cysteinyl-tRNA synthetase signature
Database References
PRINTS; PR90000 TRNASYNTH; PR90001 TRNASYNTHCLI
PROSITE; PS00178 AA_TRNA_LIGASE_I
INTERPRO; IPR002308
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 in these synthetases.
 
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.
 
Cysteinyl-tRNA synthetase (EC 6.1.1.16) is specific to cysteine and belongs
to class I.
 
TRNASYNTHCYS is a 4-element fingerprint that provides a signature for 
cysteinyl-tRNA synthetases. The fingerprint was derived from an initial
alignment of 7 sequences: the motifs were drawn from the N-terminal and
central regions of the alignment - motif 1 lies adjacent to the `HIGH'
region; and motif 5 lies next to the `KMSKS' region. Two iterations on
OWL30.2 were required to reach convergence, at which point a true set
comprising 16 sequences was identified. Several partial matches were also
found: with the exception of MTCY26124 and MTCY27037, which are cosmids 
containing partial cds, all are AATRS fragments.
 
An update on SPTR37_9f identified a true set of 22 sequences.
Summary Information
22 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
422222222
30000
20000
1234
True Positives
O33264        O51545        O58370        O67163        
O76618 O82267 O84787 Q49784
SYC_ARCFU SYC_AZOBR SYC_BACSU SYC_ECOLI
SYC_HAEIN SYC_HELPY SYC_HUMAN SYC_MYCGE
SYC_MYCPN SYC_MYCTU SYC_SYNY3 SYC_TREPA
YAF6_SCHPO YNY7_YEAST
Sequence Titles
O33264      CYSTEINYL-TRNA SYNTHETASE - MYCOBACTERIUM TUBERCULOSIS. 
O51545 CYSTEINYL-TRNA SYNTHETASE (CYSS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O58370 476AA LONG HYPOTHETICAL CYSTEINYL-TRNA SYNTHETASE - PYROCOCCUS HORIKOSHII.
O67163 CYSTEINYL-TRNA SYNTHETASE - AQUIFEX AEOLICUS.
O76618 Y23H5A.7 PROTEIN - CAENORHABDITIS ELEGANS.
O82267 PUTATIVE CYSTEINYL-TRNA SYNTHETASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O84787 CYSTEINYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
Q49784 COSMID B2126 - MYCOBACTERIUM LEPRAE.
SYC_ARCFU CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - ARCHAEOGLOBUS FULGIDUS.
SYC_AZOBR CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - AZOSPIRILLUM BRASILENSE.
SYC_BACSU CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - BACILLUS SUBTILIS.
SYC_ECOLI CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - ESCHERICHIA COLI.
SYC_HAEIN CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - HAEMOPHILUS INFLUENZAE.
SYC_HELPY CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYC_HUMAN CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - HOMO SAPIENS (HUMAN).
SYC_MYCGE CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - MYCOPLASMA GENITALIUM.
SYC_MYCPN CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - MYCOPLASMA PNEUMONIAE.
SYC_MYCTU CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - MYCOBACTERIUM TUBERCULOSIS.
SYC_SYNY3 CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
SYC_TREPA CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16) (CYSTEINE--TRNA LIGASE) (CYSRS) - TREPONEMA PALLIDUM.
YAF6_SCHPO PUTATIVE CYSTEINYL-TRNA SYNTHETASE C29E6.06C (EC 6.1.1.16) (CYSTEINE-- TRNA LIGASE) (CYSRS) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
YNY7_YEAST PUTATIVE CYSTEINYL-TRNA SYNTHETASE C29E6.06C (EC 6.1.1.16) (CYSTEINE-- TRNA LIGASE) (CYSRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
Scan History
OWL30_2    2  75   NSINGLE    
SPTR37_9f 2 23 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
MYCCGITVYDYC SYC_SYNY3 26 26 -
MYVCGPTVYNYI SYC_BACSU 26 26 -
MYVCGITVYDLC SYC_ECOLI 25 25 -
MYVCGVTVYDLC SYC_HAEIN 25 25 -
IYLCGPTVYNDL SYC_MYCPN 28 28 -
IYVCGPTVYDDA SYC_HELPY 24 24 -
IYLCGPTVYNDL SYC_MYCGE 20 20 -

Motif 2 width=10
Element Seqn Id St Int Rpt
VRYVQNFTDI SYC_SYNY3 62 24 -
VQYVSNFTDV SYC_BACSU 62 24 -
LKYVRNITDI SYC_ECOLI 61 24 -
LTYVRNITDV SYC_HAEIN 61 24 -
VQFVQNITDI SYC_MYCPN 64 24 -
VMLVRNFTDI SYC_HELPY 60 24 -
VNFVQNITDI SYC_MYCGE 56 24 -

Motif 3 width=19
Element Seqn Id St Int Rpt
EPAWESPWGKGRPGWHIEC SYC_SYNY3 197 125 -
EISWDSPWGKGRPGWHIEC SYC_BACSU 191 119 -
EPSWPSPWGAGRPGWHIEC SYC_ECOLI 191 120 -
EPSWASPWGAGRPGWHIEC SYC_HAEIN 191 120 -
GVKWNSPWGWGRPGWHVEC SYC_MYCPN 187 113 -
DVGFDSPLGKGRPGWHIEC SYC_HELPY 189 119 -
GIKWNSKWGLGRPGWHVEC SYC_MYCGE 178 112 -

Motif 4 width=22
Element Seqn Id St Int Rpt
DLHVGGNDLIFPHHENEIAQSE SYC_SYNY3 228 12 -
DIHAGGQDLTFPHHENEIAQSE SYC_BACSU 222 12 -
DIHGGGSDLMFPHHENEIAQST SYC_ECOLI 222 12 -
DIHGGGSDLMFPHHENEIAQSC SYC_HAEIN 222 12 -
TIHGGGVDLKFPHHENENAMHM SYC_MYCPN 218 12 -
DIHAGGADLLFPHHENEACQTR SYC_HELPY 225 17 -
TIHGGGVDLKFPHHENENALHM SYC_MYCGE 209 12 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
MYVCGPTVYDYP O58370 26 26 -
MYCCGITVYDYC SYC_SYNY3 26 26 -
MYVCGPTVYNYI SYC_BACSU 26 26 -
MYVCGITVYDLC SYC_ECOLI 25 25 -
MYVCGVTVYDLC SYC_HAEIN 25 25 -
MYVCGVTAYDLS O82267 88 88 -
WYSCGPTVYDAS YNY7_YEAST 60 60 -
IYTCGVTVYDDS O67163 26 26 -
WYCCGPTVYDAS SYC_HUMAN 52 52 -
MYVCGITAYDYS SYC_ARCFU 25 25 -
LYTCGPTVYDYA O84787 45 45 -
WYCCGPTVYDAS YAF6_SCHPO 43 43 -
MYVCGPTVYDTA SYC_AZOBR 26 26 -
WYICGPTVYDSS O76618 207 207 -
IYLCGPTVYNDL SYC_MYCPN 28 28 -
IYVCGPTVYDDA SYC_HELPY 24 24 -
MYVCGITPYDAT Q49784 1 1 -
MYVCGITPYDAT O33264 40 40 -
IYLCGPTVYNDL SYC_MYCGE 20 20 -
LYGCGPTVYNYP SYC_TREPA 26 26 -
IYLCGATVQGLP SYC_MYCTU 30 30 -
VYACGPTVYNYA O51545 24 24 -

Motif 2 width=10
Element Seqn Id St Int Rpt
VLMVMNFTDI O58370 62 24 -
VRYVQNFTDI SYC_SYNY3 62 24 -
VQYVSNFTDV SYC_BACSU 62 24 -
LKYVRNITDI SYC_ECOLI 61 24 -
LTYVRNITDV SYC_HAEIN 61 24 -
VSYVRNFTDV O82267 124 24 -
VQFVQNVTDI YNY7_YEAST 97 25 -
VKFVRNFTDV O67163 62 24 -
VFYCMNITDI SYC_HUMAN 89 25 -
VVYVQNFTDV SYC_ARCFU 61 24 -
VYHVMNITDV O84787 81 24 -
ITFVQNVTDI YAF6_SCHPO 80 25 -
VTYVRNITAS SYC_AZOBR 61 23 -
VEFIMNITDV O76618 244 25 -
VQFVQNITDI SYC_MYCPN 64 24 -
VMLVRNFTDI SYC_HELPY 60 24 -
VHYVQNVTDV Q49784 37 24 -
LHYVQNITDI O33264 76 24 -
VNFVQNITDI SYC_MYCGE 56 24 -
VTYVMNITDV SYC_TREPA 62 24 -
VAFIRNVTDI SYC_MYCTU 66 24 -
VNYAMNITDI O51545 60 24 -

Motif 3 width=19
Element Seqn Id St Int Rpt
EPKWESPWGEGRPGWHIEC O58370 191 119 -
EPAWESPWGKGRPGWHIEC SYC_SYNY3 197 125 -
EISWDSPWGKGRPGWHIEC SYC_BACSU 191 119 -
EPSWPSPWGAGRPGWHIEC SYC_ECOLI 191 120 -
EPSWASPWGAGRPGWHIEC SYC_HAEIN 191 120 -
EPFWESPWGRGRPGWHIEC O82267 253 119 -
EPEWESPWGKGRPGWHIEC YNY7_YEAST 351 244 -
EPAWDSPWGKGRPGWHTEC O67163 191 119 -
EPSWPCPWGKGRPGWHIEC SYC_HUMAN 330 231 -
QAVFDSPWGRGRPGWHIEC SYC_ARCFU 193 122 -
EIFWESPFGKGRPGWHLEC O84787 215 124 -
EPSWDSPWSKGRPGWHIEC YAF6_SCHPO 332 242 -
QPGWDSPWGRGRPGWHIEC SYC_AZOBR 188 117 -
EPFWPSEWGNGRPGWHIEC O76618 492 238 -
GVKWNSPWGWGRPGWHVEC SYC_MYCPN 187 113 -
DVGFDSPLGKGRPGWHIEC SYC_HELPY 189 119 -
EPSWSSPFGPGRPGWHVEC Q49784 173 126 -
EPSWPSPFGPGRPGWHVEC O33264 215 129 -
GIKWNSKWGLGRPGWHVEC SYC_MYCGE 178 112 -
ALTWDSPWGRGYPGWHIGC SYC_TREPA 209 137 -
EPSWPTPWGRGRPGWHLEC SYC_MYCTU 193 117 -
EMKWDSPWGFGYPSWHLEC O51545 203 133 -

Motif 4 width=22
Element Seqn Id St Int Rpt
DIHGGGNDLIFPHHENEIAQSE O58370 222 12 -
DLHVGGNDLIFPHHENEIAQSE SYC_SYNY3 228 12 -
DIHAGGQDLTFPHHENEIAQSE SYC_BACSU 222 12 -
DIHGGGSDLMFPHHENEIAQST SYC_ECOLI 222 12 -
DIHGGGSDLMFPHHENEIAQSC SYC_HAEIN 222 12 -
DIHGGGMDLVFPHHENEIAQSC O82267 284 12 -
DIHSGGIDLAFPHHDNELAQSE YNY7_YEAST 382 12 -
DIHGGGLDLVFPHHENEIAQAE O67163 222 12 -
DIHGGGFDLRFPHHDNELAQSE SYC_HUMAN 361 12 -
DIHGGGKDLIFPHHENERAQSF SYC_ARCFU 224 12 -
DIHAGGVDNIFPHHENEIAQSE O84787 246 12 -
DIHSGGIDLAFPHHDNELAQSE YAF6_SCHPO 363 12 -
DIHGGGLDLILPDHENEIAQSR SYC_AZOBR 219 12 -
DIHAGGFDLKFPHHDNEIAQVE O76618 523 12 -
TIHGGGVDLKFPHHENENAMHM SYC_MYCPN 218 12 -
DIHAGGADLLFPHHENEACQTR SYC_HELPY 225 17 -
DIQGGGSDLIFPHHEFTAAHAE Q49784 204 12 -
DIQGGGSDLIFPHHEFTAAHAE O33264 246 12 -
TIHGGGVDLKFPHHENENALHM SYC_MYCGE 209 12 -
DIHIGGVDHIRVHHRNERAQCE SYC_TREPA 240 12 -
DIHCGGMDLVFPHHENEIAQSR SYC_MYCTU 224 12 -
DIHLGGVDHIGVHHINEIAIAE O51545 234 12 -