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PR00980

Identifier
TRNASYNTHALA  [View Relations]  [View Alignment]  
Accession
PR00980
No. of Motifs
5
Creation Date
16-SEP-1998  (UPDATE 07-JUN-1999)
Title
Alanyl-tRNA synthetase signature
Database References
PRINTS; PR90000 TRNASYNTH; PR90002 TRNASYNTHCLII
PROSITE; PS00179 AA_TRNA_LIGASE_II_1; PS00339 AA_TRNA_LIGASE_II_2
INTERPRO; IPR002318
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.
 
Alanyl-tRNA synthetase (EC 6.1.1.7) is specific to alanine and belongs to 
class II.
 
TRNASYNTHALA is a 5-element fingerprint that provides a signature for 
alanyl-tRNA synthetases. The fingerprint was derived from an initial
alignment of 7 sequences: the motifs were drawn from the N-terminal half 
of the alignment - motif 2 includes the region encoded by PROSITE pattern
AA_TRNA_LIGASE_II_2 (PS00339). Three iterations on OWL30.2 were required
to reach convergence, at which point a true set comprising 27 sequences 
was identified. A single partial match was also found, CEU41660, a small
AATRS-like protein that lacks motifs 4 and 5.
 
An update on SPTR37_9f identified a true set of 26 sequences, and 1
partial match.
Summary Information
  26 codes involving  5 elements
0 codes involving 4 elements
1 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
52626262626
400000
311100
200000
12345
True Positives
O01541        O51238        O58035        O67323        
O84754 Q23122 SYAC_SCHPO SYAC_YEAST
SYA_ARATH SYA_ARCFU SYA_BACSU SYA_BARBA
SYA_BOMMO SYA_ECOLI SYA_HAEIN SYA_HELPY
SYA_HUMAN SYA_METJA SYA_METTH SYA_MYCGE
SYA_MYCPN SYA_MYCTU SYA_SYNY3 SYA_THETH
SYA_THIFE SYA_TREPA
True Positive Partials
Codes involving 3 elements
Q17371
Sequence Titles
O01541      SIMILAR TO AMINOACYL-TRNA SYNTHETASE - CAENORHABDITIS ELEGANS. 
O51238 ALANYL-TRNA SYNTHETASE (ALAS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O58035 915AA LONG HYPOTHETICAL ALANYL-TRNA SYNTHETASE - PYROCOCCUS HORIKOSHII.
O67323 ALANYL-TRNA SYNTHETASE - AQUIFEX AEOLICUS.
O84754 ALANYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
Q23122 W02B12.6 PROTEIN - CAENORHABDITIS ELEGANS.
SYAC_SCHPO PROBABLE ALANYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.7) (ALANINE- -TRNA LIGASE) (ALARS) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
SYAC_YEAST ALANYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
SYA_ARATH ALANYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
SYA_ARCFU ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - ARCHAEOGLOBUS FULGIDUS.
SYA_BACSU ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - BACILLUS SUBTILIS.
SYA_BARBA ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - BARTONELLA BACILLIFORMIS.
SYA_BOMMO ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - BOMBYX MORI (SILK MOTH).
SYA_ECOLI ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - ESCHERICHIA COLI.
SYA_HAEIN ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - HAEMOPHILUS INFLUENZAE.
SYA_HELPY ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYA_HUMAN ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - HOMO SAPIENS (HUMAN).
SYA_METJA ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - METHANOCOCCUS JANNASCHII.
SYA_METTH ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
SYA_MYCGE ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - MYCOPLASMA GENITALIUM.
SYA_MYCPN ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - MYCOPLASMA PNEUMONIAE.
SYA_MYCTU ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - MYCOBACTERIUM TUBERCULOSIS.
SYA_SYNY3 ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
SYA_THETH ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
SYA_THIFE ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - THIOBACILLUS FERROOXIDANS.
SYA_TREPA ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS) - TREPONEMA PALLIDUM.

Q17371 ALARS A - CAENORHABDITIS ELEGANS.
Scan History
OWL30_2    3  40   NSINGLE    
SPTR37_9f 2 31 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
NDLENVGYTARH SYA_ECOLI 76 76 -
NDLDNVGYTARH SYA_BARBA 75 75 -
NDLENVGYTARH SYA_HAEIN 75 75 -
NDLDDVGKDTYH SYA_ARATH 137 137 -
NDLDDVGKDVYH SYA_BOMMO 83 83 -
NDIENVGRTARH SYA_SYNY3 76 76 -
NDIENVGFTSRH SYA_MYCGE 72 72 -

Motif 2 width=12
Element Seqn Id St Int Rpt
IEIWNIVFMQFN SYA_ECOLI 209 121 -
IEIWNLVFMQYE SYA_BARBA 199 112 -
IEIWNVVFMQFN SYA_HAEIN 208 121 -
LEIWNLVFIQFN SYA_ARATH 265 116 -
LEIWNLVFIQFN SYA_BOMMO 212 117 -
IEFYNLVFMQYN SYA_SYNY3 198 110 -
VEIWNIVFSQFN SYA_MYCGE 198 114 -

Motif 3 width=14
Element Seqn Id St Int Rpt
DTGMGLERIAAVLQ SYA_ECOLI 236 15 -
DTGMGLERIAAVLQ SYA_BARBA 226 15 -
DTGMGLERISAVLQ SYA_HAEIN 235 15 -
DTGMGFERLTSVLQ SYA_ARATH 292 15 -
DCGLGLERLVSVIQ SYA_BOMMO 239 15 -
DTGMGLERMAQILQ SYA_SYNY3 225 15 -
DTGAGIERLVSVLQ SYA_MYCGE 225 15 -

Motif 4 width=17
Element Seqn Id St Int Rpt
RVIADHIRSCAFLIADG SYA_ECOLI 282 32 -
RVIADHLRSSAFLIADG SYA_BARBA 274 34 -
RVIADHIRSCAYLIADG SYA_HAEIN 281 32 -
RVVADHIRTLSFAIADG SYA_ARATH 349 43 -
RVLADHARTLTIALSDG SYA_BOMMO 296 43 -
KVIGDHVRSVVHMIADG SYA_SYNY3 276 37 -
RIIADHFKAITFTISEG SYA_MYCGE 284 45 -

Motif 5 width=14
Element Seqn Id St Int Rpt
RGYVLRRIIRRAVR SYA_ECOLI 306 7 -
RGYVLRRIMRRAMR SYA_BARBA 298 7 -
RGYVLRRIIRRAVR SYA_HAEIN 305 7 -
REYVLRRILRRAVR SYA_ARATH 373 7 -
RGYVLRRILRRAVR SYA_BOMMO 320 7 -
RGYVLRRLIRRVVR SYA_SYNY3 300 7 -
RNYVVRRLLRRALI SYA_MYCGE 308 7 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
NDLENVGYTARH SYA_ECOLI 76 76 -
NDLEQVGYTSRH O67323 76 76 -
NDLENVGYTARH SYA_THIFE 74 74 -
NDLDNVGYTARH SYA_BARBA 75 75 -
NDLENVGYTARH SYA_HAEIN 75 75 -
NDLDDVGKDVYH SYA_HUMAN 83 83 -
NDLEDVGKDSYH SYAC_YEAST 87 87 -
NDLDDVGKDTYH SYA_ARATH 137 137 -
NDLENVGYTARH SYA_HELPY 71 71 -
NDIENVGKTARH SYA_BACSU 73 73 -
NDLEDVGKDNYH SYAC_SCHPO 88 88 -
NDLDDVGKDVYH SYA_BOMMO 83 83 -
NDLENVGHTSRH O84754 123 123 -
NDLDDVGKDVYH O01541 83 83 -
GDIENVGRTSRH SYA_THETH 74 74 -
NDIENVGRTARH SYA_SYNY3 76 76 -
NDIENVGFTSRH SYA_MYCGE 72 72 -
PDIDEVGITTRH SYA_MYCTU 69 69 -
NDIENVGFTSRH SYA_MYCPN 72 72 -
GDIDAVGDNSHL SYA_TREPA 74 74 -
NDVDNVGRTGRH SYA_METTH 125 125 -
GDIDEVGDLSHL O51238 70 70 -
TDIDNVGITGRH O58035 130 130 -
NDLDDVGKDLHH Q23122 94 94 -
NDIDNVGRTGRH SYA_METJA 128 128 -
DDLDSVGRTGRH SYA_ARCFU 130 130 -

Motif 2 width=12
Element Seqn Id St Int Rpt
IEIWNIVFMQFN SYA_ECOLI 209 121 -
LEIWNLVFMQYN O67323 191 103 -
IEIWNLVFMQFD SYA_THIFE 198 112 -
IEIWNLVFMQYE SYA_BARBA 199 112 -
IEIWNVVFMQFN SYA_HAEIN 208 121 -
LEIWNLVFIQYN SYA_HUMAN 212 117 -
LEVWNLVFIQFN SYAC_YEAST 216 117 -
LEIWNLVFIQFN SYA_ARATH 265 116 -
LEIWNLVFMQYE SYA_HELPY 193 110 -
LEVWNLVFSEFN SYA_BACSU 199 114 -
LEIWNIVFIQFN SYAC_SCHPO 217 117 -
LEIWNLVFIQFN SYA_BOMMO 212 117 -
LEYWNLVFMEFN O84754 245 110 -
VEIWNLVFIQFN O01541 212 117 -
VEIWNLVFTQYD SYA_THETH 204 118 -
IEFYNLVFMQYN SYA_SYNY3 198 110 -
VEIWNIVFSQFN SYA_MYCGE 198 114 -
LEVWNLVFMQNE SYA_MYCTU 196 115 -
VEVWNIVFSQFN SYA_MYCPN 198 114 -
VEIWNDVFMQYR SYA_TREPA 204 118 -
VELATLVFIQYR SYA_METTH 203 66 -
FEIWNNVFMQYN O51238 200 118 -
LEVATLVFMQYK O58035 209 67 -
VEIWNIVFMSSV Q23122 222 116 -
VELATLVFMQYE SYA_METJA 206 66 -
LEVATLVFMNLE SYA_ARCFU 208 66 -

Motif 3 width=14
Element Seqn Id St Int Rpt
DTGMGLERIAAVLQ SYA_ECOLI 236 15 -
DTGMGLERIASVLQ O67323 218 15 -
DTGMGLERLAAVLQ SYA_THIFE 225 15 -
DTGMGLERIAAVLQ SYA_BARBA 226 15 -
DTGMGLERISAVLQ SYA_HAEIN 235 15 -
DTGMGLERLVSVLQ SYA_HUMAN 239 15 -
DTGMGFERLVSVLQ SYAC_YEAST 243 15 -
DTGMGFERLTSVLQ SYA_ARATH 292 15 -
DTGMGLERVQALLE SYA_HELPY 220 15 -
DTGMGLERMVSVIQ SYA_BACSU 226 15 -
DTGMGFERLVSVIQ SYAC_SCHPO 244 15 -
DCGLGLERLVSVIQ SYA_BOMMO 239 15 -
DTGAGLERLVSLLA O84754 272 15 -
DCGLGLERLIAVMQ O01541 239 15 -
DTGMGLYRVAAILQ SYA_THETH 235 19 -
DTGMGLERMAQILQ SYA_SYNY3 225 15 -
DTGAGIERLVSVLQ SYA_MYCGE 225 15 -
DTGMGVERIALVLQ SYA_MYCTU 229 21 -
DTGAGIERLVAILQ SYA_MYCPN 225 15 -
DTGMGIERTVAVLQ SYA_TREPA 231 15 -
DTGYGLERFAWISQ SYA_METTH 230 15 -
DTGMGLERTIAFLQ O51238 227 15 -
DTGYGLERLVWMSQ O58035 248 27 -
DTGMGFERLLSVVQ Q23122 249 15 -
DTGYGIERFVWAST SYA_METJA 232 14 -
DTGYGLERFVWASK SYA_ARCFU 242 22 -

Motif 4 width=17
Element Seqn Id St Int Rpt
RVIADHIRSCAFLIADG SYA_ECOLI 282 32 -
RVIADHLRAITFAISDG O67323 268 36 -
RVLADHIRACSFLITDG SYA_THIFE 275 36 -
RVIADHLRSSAFLIADG SYA_BARBA 274 34 -
RVIADHIRSCAYLIADG SYA_HAEIN 281 32 -
RVLADHARTITVALADG SYA_HUMAN 296 43 -
RVLADHVRTLTFALADG SYAC_YEAST 300 43 -
RVVADHIRTLSFAIADG SYA_ARATH 349 43 -
RVVADHARAVAFLLAQG SYA_HELPY 268 34 -
KVIADHIRTVAFAVSDG SYA_BACSU 276 36 -
RVVADHVRTLTFAISDG SYAC_SCHPO 301 43 -
RVLADHARTLTIALSDG SYA_BOMMO 296 43 -
RVIADHIRSLSFAIADG O84754 322 36 -
RVVADHVRTLTIALSDG O01541 296 43 -
RVIADHVRAVVAALSDG SYA_THETH 283 34 -
KVIGDHVRSVVHMIADG SYA_SYNY3 276 37 -
RIIADHFKAITFTISEG SYA_MYCGE 284 45 -
RIIADHSRTAAILIGDG SYA_MYCTU 280 37 -
RIISDHFKAITFTIAEG SYA_MYCPN 284 45 -
RIVCDHIRAATFILGDP SYA_TREPA 281 36 -
YAIADHTRCLAFMLADG SYA_METTH 320 76 -
RIISDHVKAACFILADS O51238 277 36 -
YAIADHTKALTFMLADG O58035 339 77 -
RLVADHIRAATVAISDG Q23122 301 38 -
YAIVDHTRALAFMLGDG SYA_METJA 323 77 -
YSLADHTRCILFMLGDG SYA_ARCFU 338 82 -

Motif 5 width=14
Element Seqn Id St Int Rpt
RGYVLRRIIRRAVR SYA_ECOLI 306 7 -
RGYVIRRILRRAMR O67323 292 7 -
RGYVLRRIIRRAVR SYA_THIFE 299 7 -
RGYVLRRIMRRAMR SYA_BARBA 298 7 -
RGYVLRRIIRRAVR SYA_HAEIN 305 7 -
RGYVLRRILRRAVR SYA_HUMAN 320 7 -
RGYVLRRILRRGAR SYAC_YEAST 324 7 -
REYVLRRILRRAVR SYA_ARATH 373 7 -
RGYVLRRILRRALR SYA_HELPY 292 7 -
RGYVLRRLLRRAVR SYA_BACSU 300 7 -
RGYVLRRILRRGAR SYAC_SCHPO 325 7 -
RGYVLRRILRRAVR SYA_BOMMO 320 7 -
RGYVLRKILRRAVN O84754 346 7 -
RGYVLRRILRRGVR O01541 320 7 -
RGYVIRRLLRRALR SYA_THETH 307 7 -
RGYVLRRLIRRVVR SYA_SYNY3 300 7 -
RNYVVRRLLRRALI SYA_MYCGE 308 7 -
RGYVLRRLLRRVIR SYA_MYCTU 304 7 -
RSYIVRRLLRRALL SYA_MYCPN 308 7 -
AGYVLRRIIRRSVR SYA_TREPA 307 9 -
EGYLARLIIRRTLR SYA_METTH 344 7 -
QGYVLRRLIRRSIR O51238 303 9 -
AGYLARLLIRKSIR O58035 363 7 -
CGFIVRKMMRRAFL Q23122 325 7 -
DGYLVRMLIRKTLR SYA_METJA 347 7 -
AGYLARLMIRRSLR SYA_ARCFU 362 7 -