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PR01044

Identifier
TRNASYNTHGA  [View Relations]  [View Alignment]  
Accession
PR01044
No. of Motifs
6
Creation Date
14-DEC-1998  (UPDATE 07-JUN-1999)
Title
Glycyl-tRNA synthetase alpha subunit signature
Database References
PRINTS; PR90000 TRNASYNTH; PR90002 TRNASYNTHCLII; PR90003 TRNASYNTHGF
PRINTS; PR90004 TRNASYNTHGTET
PROSITE; PS00179 AA_TRNA_LIGASE_II_1; PS00339 AA_TRNA_LIGASE_II_2
INTERPRO; IPR002310
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).
 
4. WEBSTER, T.A., GIBSON, B.W., KENG, T., BIEMANN, K. AND SCHIMMEL, P.
Primary Structures of Both Subunits of Escherichia coli Glycyl-tRNA
Synthetase.
J.BIOL.CHEM. 258(17) 10637-10641 (1983).
 
5. SHIBA, K., SCHIMMEL, P., MOTEGI, H. AND NODA, T.
Human Glycyl-tRNA Synthetase.
J.BIOL.CHEM. 269(47) 30049-30055 (1994).
 
6. WAGAR, E.A., GIESE, M.J., YASIN, B. AND PANG, M.
The Gylcyl-tRNA Synthetase of Chlamydia trachomatis.
J.BACTERIOL. 177(17) 5179-5185 (1995).

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.
 
Glycyl-tRNA synthetase (EC 6.1.1.14) is specific to glycine and belongs to
class II. It is one of the most complex synthetases, existing as either an
alpha(2) dimer or alpha(2)-beta(2) tetramer [4-6]. What is most interesting
is the lack of similarity between the two types: divergence at the sequence
level is so great that it is impossible to infer descent from common genes. 
The alpha and beta subunits also lack significant sequence similarity.
However, they are translated from a single mRNA [4], and a single chain 
glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have 
significant similarity with both domains, suggesting divergence from a 
single polypeptide chain [6].
 
TRNASYNTHGA is a 6-element fingerprint that provides a signature for the
glycyl-tRNA synthetase alpha subunit. The fingerprint was derived from an
initial alignment of 5 sequences: the motifs were drawn from conserved
regions spanning the full alignment length - motif 5 includes the region
encoded by PROSITE pattern AA_TRNA_LIGASE_II_2 (PS00339). Two iterations 
on OWL30.2 were required to reach convergence, at which point a true set
comprising 11 sequences was identified. A single partial match was found,
PFY145682, a fragment that lacks the portion of sequence bearing motif 6.
 
An update on SPTR37_9f identified a true set of 11 sequences.
Summary Information
11 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6111111111111
5000000
4000000
3000000
2000000
123456
True Positives
O23150        O67081        O84802        P94616        
SYGA_BACSU SYGA_ECOLI SYGA_HAEIN SYGA_HELPY
SYGA_MORCA SYGA_SYNY3 SYG_CHLTR
Sequence Titles
O23150      AMINOACYL-T-RNA SYNTHETASE PRECURSOR - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). 
O67081 GLYCYL-TRNA SYNTHETASE ALPHA SUBUNIT - AQUIFEX AEOLICUS.
O84802 GLYCYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
P94616 SIMILARITY TO SWISS-PROT: SYGA_ECOLI GLYCYL-TRNA SYNTHETASE ALPHA-CHAIN - COXIELLA BURNETII.
SYGA_BACSU GLYCYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE ALPHA CHAIN) (GLYRS) - BACILLUS SUBTILIS.
SYGA_ECOLI GLYCYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE ALPHA CHAIN) (GLYRS) - ESCHERICHIA COLI.
SYGA_HAEIN GLYCYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE ALPHA CHAIN) (GLYRS) - HAEMOPHILUS INFLUENZAE.
SYGA_HELPY GLYCYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE ALPHA CHAIN) (GLYRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYGA_MORCA GLYCYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE ALPHA CHAIN) (GLYRS) - MORAXELLA CATARRHALIS.
SYGA_SYNY3 GLYCYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE ALPHA CHAIN) (GLYRS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
SYG_CHLTR GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - CHLAMYDIA TRACHOMATIS.
Scan History
OWL30_2    2  40   NSINGLE    
SPTR37_9f 2 12 NSINGLE
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
PSRRPTDGRYGENPNR SYGA_HAEIN 62 62 -
PSRRPTDGRYGENPNR SYGA_ECOLI 61 61 -
PSRRPTDGRYGDNPNR SYGA_MORCA 61 61 -
PSRRPADGRYGENPNR SYGA_BACSU 55 55 -
PCRRPTDGRYGENPNR SYGA_SYNY3 57 57 -

Motif 2 width=21
Element Seqn Id St Int Rpt
QFQVIIKPSPDNIQELYLDSL SYGA_BACSU 76 5 -
QFQVVIKPSPDNIQELYLGSL SYGA_ECOLI 82 5 -
QFQVVIKPSPDNIQELYLGSL SYGA_HAEIN 83 5 -
QFQVVLKPNPANIQELYLGSL SYGA_MORCA 82 5 -
QYQVLIKPSPDNIQEVYLDSL SYGA_SYNY3 78 5 -

Motif 3 width=25
Element Seqn Id St Int Rpt
DIRFVEDNWESPTLGAWGVGWEVWL SYGA_SYNY3 109 10 -
DIRFVEDNWENPTLGAWGLGWEVWL SYGA_ECOLI 113 10 -
DIRFVEDNWENPTLGAWGLGWEVWL SYGA_HAEIN 114 10 -
DVRFVEDNWESPTLGAWGLGWEVWL SYGA_MORCA 113 10 -
DIRFVEDNWENPSLGCAGLGWEVWL SYGA_BACSU 107 10 -

Motif 4 width=21
Element Seqn Id St Int Rpt
GMEVTQFTYFQQCGGIDCRPV SYGA_SYNY3 135 1 -
GMEVTQFTYFQQVGGLECKPV SYGA_ECOLI 139 1 -
GMEVTQFTYFQQVGGLECKPV SYGA_HAEIN 140 1 -
GMEVTQFTYFQQVGGIECFPV SYGA_MORCA 139 1 -
GMEITQFTYFQQVGGLECKPV SYGA_BACSU 133 1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
EITYGLERLAMYIQGV SYGA_ECOLI 162 2 -
EVTYGLERLAMYIQGV SYGA_HAEIN 163 2 -
EITYGLERLAMYIQGV SYGA_MORCA 162 2 -
EITYGIERLASYIQDK SYGA_BACSU 156 2 -
EITYGLERLAMYLQNV SYGA_SYNY3 158 2 -

Motif 6 width=17
Element Seqn Id St Int Rpt
HSFNLLDARKAISVTER SYGA_ECOLI 253 75 -
HSFNLLDARKAISVTER SYGA_HAEIN 254 75 -
HAFNLLDARGAISVTER SYGA_MORCA 251 73 -
HTFNLLDAKGAISVTER SYGA_BACSU 241 69 -
HAFNLLDARGVIAVTER SYGA_SYNY3 243 69 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
PSRRPTDGRYGENPNR SYGA_HAEIN 62 62 -
PSRRPTDGRYGENPNR SYGA_ECOLI 61 61 -
PSRRPTDGRYGDNPNR SYGA_MORCA 61 61 -
PSRRPTDGRYGENPNR SYGA_HELPY 56 56 -
PSRRPADGRYGENPNR SYGA_BACSU 55 55 -
PCRRPTDGRYGENPNR SYGA_SYNY3 57 57 -
PSRRPQDGRYGENPNR O67081 55 55 -
PSRRPTDGRYGDNPNR P94616 61 61 -
PSRRPQDGRYGQHPNR O84802 60 60 -
PSRRPQDGRYGQHPNR SYG_CHLTR 60 60 -
PSIRPDDSRYGENPNR O23150 125 125 -

Motif 2 width=21
Element Seqn Id St Int Rpt
QLQVILKPVPENFLSLYLESL SYG_CHLTR 81 5 -
QFQVVIKPSPDNIQELYLGSL SYGA_ECOLI 82 5 -
QFQVVIKPSPDNIQELYLGSL SYGA_HAEIN 83 5 -
QFQVVLKPNPANIQELYLGSL SYGA_MORCA 82 5 -
QFQVVIKPSPSNIQELYLKSL SYGA_HELPY 77 5 -
QFQVIIKPSPDNIQELYLDSL SYGA_BACSU 76 5 -
QYQVLIKPSPDNIQEVYLDSL SYGA_SYNY3 78 5 -
QFQVILKPAPRNPQEIYLESL O67081 76 5 -
QFQVVLKPSPDDIQDIYLGSL P94616 82 5 -
QLQVILKPVPENFLSLYLESL O84802 81 5 -
QFQVILKPDPGNSQQLFINSL O23150 146 5 -

Motif 3 width=25
Element Seqn Id St Int Rpt
DVRFVEDNWESPTLGAWGLGWEVWL SYGA_MORCA 113 10 -
DIRFVEDNWENPTLGAWGLGWEVWL SYGA_ECOLI 113 10 -
DIRFVEDNWENPTLGAWGLGWEVWL SYGA_HAEIN 114 10 -
DIRFVEDNWESPTLGAWGLGWEVWL SYGA_HELPY 108 10 -
DIRFVEDNWENPSLGCAGLGWEVWL SYGA_BACSU 107 10 -
DIRFVEDNWESPTLGAWGVGWEVWL SYGA_SYNY3 109 10 -
DIRFVEDDWESPTLGAWGLGWEVWL O67081 107 10 -
DIRFVEDNWEAPTLGSWGVGWEVWQ P94616 113 10 -
DIRFVHDDWENPTIGAWGLGWEVWL O84802 112 10 -
DIRFVHDDWENPTIGAWGLGWEVWL SYG_CHLTR 112 10 -
DIRFVEDNWESPVLGAWGLGWEIWM O23150 177 10 -

Motif 4 width=21
Element Seqn Id St Int Rpt
GMEVTQFTYFQQVGGLECKPV SYGA_ECOLI 139 1 -
GMEVTQFTYFQQVGGLECKPV SYGA_HAEIN 140 1 -
GMEVTQFTYFQQVGGIECFPV SYGA_MORCA 139 1 -
GMEVTQFTYFQQVGGIACSPI SYGA_HELPY 134 1 -
GMEITQFTYFQQVGGLECKPV SYGA_BACSU 133 1 -
GMEVTQFTYFQQCGGIDCRPV SYGA_SYNY3 135 1 -
GMEITQFTYFQQAGGLDLDEI O67081 133 1 -
GMEITQFTYFQQIGGLECKPV P94616 139 1 -
GMEITQLTYFQAVGSKPLDAI O84802 138 1 -
GMEITQLTYFQAVGSKPLDAI SYG_CHLTR 138 1 -
GMEITQFTYFQQAGSLPLSPV O23150 203 1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
EITYGLERIIMLLQEV O23150 226 2 -
EVTYGLERLAMYIQGV SYGA_HAEIN 163 2 -
EITYGLERLAMYIQGV SYGA_MORCA 162 2 -
EITYGLERLAMYIQGV SYGA_ECOLI 162 2 -
EITYGLERLAMYVQKV SYGA_HELPY 157 2 -
EITYGIERLASYIQDK SYGA_BACSU 156 2 -
EITYGLERLAMYLQNV SYGA_SYNY3 158 2 -
EITYGLERIAMYIQDK O67081 156 2 -
EITYGLERLAMFLQGI P94616 162 2 -
EITYGVERIAMYLQKK O84802 161 2 -
EITYGVERIAMYLQKK SYG_CHLTR 161 2 -

Motif 6 width=17
Element Seqn Id St Int Rpt
HAFNMLDSRGVISVTER SYG_CHLTR 246 69 -
HSFNLLDARKAISVTER SYGA_ECOLI 253 75 -
HSFNLLDARKAISVTER SYGA_HAEIN 254 75 -
HAFNLLDARGAISVTER SYGA_MORCA 251 73 -
HFFNILDARKAISVAER SYGA_HELPY 246 73 -
HTFNLLDAKGAISVTER SYGA_BACSU 241 69 -
HAFNLLDARGVIAVTER SYGA_SYNY3 243 69 -
HVFNILDARGAISVQER O67081 241 69 -
HTFNLLDARQAISVTER P94616 251 73 -
HAFNMLDSRGVISVTER O84802 246 69 -
HAFNILDARGFIGVTER O23150 311 69 -