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PR01045

Identifier
TRNASYNTHGB  [View Relations]  [View Alignment]  
Accession
PR01045
No. of Motifs
5
Creation Date
14-DEC-1998  (UPDATE 07-JUN-1999)
Title
Glycyl-tRNA synthetase beta 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; IPR002311
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].
 
TRNASYNTHGB is a 5-element fingerprint that provides a signature for the
glycyl-tRNA synthetase beta subunit. The fingerprint was derived from an
initial alignment of 5 sequences: the motifs were drawn from conserved
regions spanning the full alignment length. Three iterations on OWL31.1
were required to reach convergence, at which point a true set comprising 10
sequences was identified. Two partial matches were also found, SYGB_MORCA
and CBGTSAB1, both of which are beta subunit fragments.
 
An update on SPTR37_9f identified a true set of 9 sequences.
Summary Information
9 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
599999
400000
300000
200000
12345
True Positives
O23150        O67898        O84802        SYGB_BACSU    
SYGB_ECOLI SYGB_HAEIN SYGB_HELPY SYGB_SYNY3
SYG_CHLTR
Sequence Titles
O23150      AMINOACYL-T-RNA SYNTHETASE PRECURSOR - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). 
O67898 GLYCYL-TRNA SYNTHETASE BETA SUBUNIT - AQUIFEX AEOLICUS.
O84802 GLYCYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
SYGB_BACSU GLYCYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE BETA CHAIN) (GLYRS) - BACILLUS SUBTILIS.
SYGB_ECOLI GLYCYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE BETA CHAIN) (GLYRS) - ESCHERICHIA COLI.
SYGB_HAEIN GLYCYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE BETA CHAIN) (GLYRS) - HAEMOPHILUS INFLUENZAE.
SYGB_HELPY GLYCYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE BETA CHAIN) (GLYRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYGB_SYNY3 GLYCYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.14) (GLYCINE--TRNA LIGASE BETA 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
OWL31_1    3  50   NSINGLE    
SPTR37_9f 2 10 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
LFEIGTEELPADFV SYGB_SYNY3 7 7 -
LLEIGLEEMPARFL SYGB_BACSU 7 7 -
LVEIGTEELPPKAL SYGB_HAEIN 7 7 -
LVEIGTEELPPKAL SYGB_ECOLI 6 6 -
LVEILVEELPAQAL SYGB_HELPY 7 7 -

Motif 2 width=13
Element Seqn Id St Int Rpt
TPRRLAVLIKGLP SYGB_SYNY3 50 29 -
TPRRLAVFVKDVA SYGB_BACSU 50 29 -
APRRLAVKVLNLA SYGB_HAEIN 50 29 -
APRRLALKVANLA SYGB_ECOLI 49 29 -
TPRRLCLLIKDFP SYGB_HELPY 50 29 -

Motif 3 width=16
Element Seqn Id St Int Rpt
DLLDEVEQLVEYPTAV SYGB_SYNY3 248 185 -
DLLDEVNHLVEYPTAL SYGB_BACSU 243 180 -
SLLEEVTSLVEYPNVL SYGB_HAEIN 246 183 -
SLLEEVASLVEWPVVL SYGB_ECOLI 245 183 -
DLLDEVVAITEYPSAL SYGB_HELPY 252 189 -

Motif 4 width=17
Element Seqn Id St Int Rpt
GNGRVIRARLADAKFFY SYGB_SYNY3 320 56 -
GNEKVLRARLSDASFFY SYGB_BACSU 315 56 -
GNEKVVRPRLTDAEFFF SYGB_HAEIN 318 56 -
GNEKVVRPRLADAEFFF SYGB_ECOLI 317 56 -
GNQKVLKARLSDAVFFY SYGB_HELPY 329 61 -

Motif 5 width=20
Element Seqn Id St Int Rpt
KADLVTQMVYEFPELQGIMG SYGB_SYNY3 399 62 -
KFDLVTHMIYEFPELQGIMG SYGB_BACSU 394 62 -
KCDLMTNMVFEFTDTQGVMG SYGB_HAEIN 394 59 -
KCDLMTNMVFEFTDTQGVMG SYGB_ECOLI 393 59 -
KADLLSEVVYEFSELQGIMG SYGB_HELPY 411 65 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
LFEIGTEELPADFV SYGB_SYNY3 7 7 -
LLEIGLEEMPARFL SYGB_BACSU 7 7 -
LVEIGTEELPPKAL SYGB_HAEIN 7 7 -
LVEIGTEELPPKAL SYGB_ECOLI 6 6 -
LLEIGSEELPATFV SYG_CHLTR 316 316 -
LLEIGSEELPATFV O84802 316 316 -
LVEILVEELPAQAL SYGB_HELPY 7 7 -
LIEIGTEELPAGVI O67898 6 6 -
IIEIGTEEMPPQDV O23150 387 387 -

Motif 2 width=13
Element Seqn Id St Int Rpt
TPRRLAVLIKGLP SYGB_SYNY3 50 29 -
TPRRLAVFVKDVA SYGB_BACSU 50 29 -
APRRLAVKVLNLA SYGB_HAEIN 50 29 -
APRRLALKVANLA SYGB_ECOLI 49 29 -
TPRRLALCIEGLS SYG_CHLTR 359 29 -
TPRRLALCIEGLS O84802 359 29 -
TPRRLCLLIKDFP SYGB_HELPY 50 29 -
TPRRLTLYFKDFE O67898 44 24 -
TPRRLVVLVDAMS O23150 430 29 -

Motif 3 width=16
Element Seqn Id St Int Rpt
DLLDEVEQLVEYPTAV SYGB_SYNY3 248 185 -
DLLDEVNHLVEYPTAL SYGB_BACSU 243 180 -
SLLEEVTSLVEYPNVL SYGB_HAEIN 246 183 -
SLLEEVASLVEWPVVL SYGB_ECOLI 245 183 -
HLVDETVFLTEHPFVI SYG_CHLTR 563 191 -
HLIDETVFLTEHPFVI O84802 563 191 -
DLLDEVVAITEYPSAL SYGB_HELPY 252 189 -
GLVEEVTNLVEYPFPV O67898 240 183 -
NLLNEVANLVEAPVPL O23150 624 181 -

Motif 4 width=17
Element Seqn Id St Int Rpt
GNGRVIRARLADAKFFY SYGB_SYNY3 320 56 -
GNEKVLRARLSDASFFY SYGB_BACSU 315 56 -
GNEKVVRPRLTDAEFFF SYGB_HAEIN 318 56 -
GNEKVVRPRLADAEFFF SYGB_ECOLI 317 56 -
GNEKALAPRLTDGNFLF SYG_CHLTR 633 54 -
GNEKALAPRLTDGNFLF O84802 633 54 -
GNQKVLKARLSDAVFFY SYGB_HELPY 329 61 -
GYEKVLRARLEDALFFY O67898 309 53 -
GNEAVLRARYEDAKFFY O23150 695 55 -

Motif 5 width=20
Element Seqn Id St Int Rpt
KADLVTQMVYEFPELQGIMG SYGB_SYNY3 399 62 -
KFDLVTHMIYEFPELQGIMG SYGB_BACSU 394 62 -
KCDLMTNMVFEFTDTQGVMG SYGB_HAEIN 394 59 -
KCDLMTNMVFEFTDTQGVMG SYGB_ECOLI 393 59 -
KADLVSSVVNEFPELQGIMG SYG_CHLTR 710 60 -
KADLVSSVVNEFPELQGIMG O84802 710 60 -
KADLLSEVVYEFSELQGIMG SYGB_HELPY 411 65 -
KVDLLTEMVKELDELQGYMG O67898 385 59 -
MSDLATAVVTEFTALSGIMA O23150 774 62 -