EzCatDB: D00295
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DB codeD00295
RLCP classification3.113.90030.2130 : Transfer
CATH domainDomain 13.30.930.10 : BirA Bifunctional Protein; domain 2Catalytic domain
Domain 23.40.50.800 : Rossmann fold
E.C.6.1.1.14

CATH domainRelated DB codes (homologues)
3.30.930.10 : BirA Bifunctional Protein; domain 2S00413,D00291,D00293,D00294,M00049,T00113
3.40.50.800 : Rossmann foldM00049

Enzyme Name
UniProtKBKEGG

P56206
Protein nameGlycyl-tRNA synthetaseglycine---tRNA ligase
glycyl-tRNA synthetase
glycyl-transfer ribonucleate synthetase
glycyl-transfer RNA synthetase
glycyl-transfer ribonucleic acid synthetase
glycyl translase
SynonymsEC 6.1.1.14
Glycine--tRNA ligase
GlyRS
RefSeqYP_143809.1 (Protein)
NC_006461.1 (DNA/RNA sequence)
PfamPF03129 (HGTP_anticodon)
PF00587 (tRNA-synt_2b)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism
MAP00970Aminoacyl-tRNA biosynthesis

UniProtKB:Accession NumberP56206
Entry nameSYG_THET8
ActivityATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
SubunitHomodimer.
Subcellular locationCytoplasm.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00305C00002C00037C01642C00020C00013C02412
CompoundMagnesiumATPGlycinetRNA(Gly)AMPPyrophosphateGlycyl-tRNA(Gly)Glycyl-adenylate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acidsnucleic acidsamine group,nucleotidephosphate group/phosphate ionamino acids,nucleic acids
ChEBI18420
15422
15428
57305

16027
29888


PubChem888
5957
750
5257127

6083
21961011
1023


                
1atiA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1atiB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b76A01UnboundBound:ATPUnboundUnboundUnboundUnboundUnboundUnbound
1b76B01UnboundBound:ATPUnboundUnboundUnboundUnboundUnboundUnbound
1ggmA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:GAP
1ggmB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:GAP
1atiA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1atiB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b76A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b76B02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ggmA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ggmB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [7] & [10]
pdbCatalytic residuesCofactor-binding residues
          
1atiA01ARG 220;ARG 231;ARG 366
ASP 293;GLU 304(magnesium binding)
1atiB01ARG 220;ARG 231;ARG 366
ASP 293;GLU 304(magnesium binding)
1b76A01ARG 220;ARG 231;ARG 366
ASP 293;GLU 304(magnesium binding)
1b76B01ARG 220;ARG 231;ARG 366
ASP 293;GLU 304(magnesium binding)
1ggmA01ARG 220;ARG 231;ARG 366
ASP 293;GLU 304(magnesium binding)
1ggmB01ARG 220;ARG 231;ARG 366
ASP 293;GLU 304(magnesium binding)
1atiA02 
 
1atiB02 
 
1b76A02 
 
1b76B02 
 
1ggmA02 
 
1ggmB02 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p.4158
[7]p.346-348
[10]Fig.5, p.14552

references
[1]
PubMed ID6262123
JournalFEBS Lett
Year1981
Volume124
Pages293-8
AuthorsLed JJ, Andersen AJ
TitleThe use of paramagnetic 13C NMR relaxation to study the mechanisms of the amino acid activation catalysed by a cognate tRNA synthetase.
[2]
PubMed ID6315429
JournalEur J Biochem
Year1983
Volume136
Pages469-79
AuthorsLed JJ, Switon WK, Jensen KF
TitlePhosphorolytic activity of Escherichia coli glycyl-tRNA synthetase towards its cognate aminoacyl adenylate detected by 31P-NMR spectroscopy and thin-layer chromatography.
[3]
PubMed ID1546312
JournalScience
Year1992
Volume255
Pages1121-5
AuthorsFrancklyn C, Shi JP, Schimmel P
TitleOverlapping nucleotide determinants for specific aminoacylation of RNA microhelices.
[4]
PubMed ID8071996
JournalJ Mol Biol
Year1994
Volume241
Pages732-5
AuthorsLogan DT, Cura V, Touzel JP, Kern D, Moras D
TitleCrystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and initial crystallographic data.
[5]
PubMed ID8845358
JournalBiochemistry
Year1995
Volume34
Pages16327-36
AuthorsWu H, Nada S, Dignam JD
TitleAnalysis of truncated forms of Bombyx mori glycyl-tRNA synthetase: function of an N-terminal structure in RNA binding.
[6]
CommentsX-ray crystallography
PubMed ID7556056
JournalEMBO J
Year1995
Volume14
Pages4156-67
AuthorsLogan DT, Mazauric MH, Kern D, Moras D
TitleCrystal structure of glycyl-tRNA synthetase from Thermus thermophilus.
Related PDB1ati
[7]
PubMed ID8839980
JournalBiol Chem Hoppe Seyler
Year1996
Volume377
Pages343-56
AuthorsFreist W, Logan DT, Gauss DH
TitleGlycyl-tRNA synthetase.
[8]
PubMed ID8944770
JournalEur J Biochem
Year1996
Volume241
Pages814-26
AuthorsMazauric MH, Reinbolt J, Lorber B, Ebel C, Keith G, Giege R, Kern D
TitleAn example of non-conservation of oligomeric structure in prokaryotic aminoacyl-tRNA synthetases. Biochemical and structural properties of glycyl-tRNA synthetase from Thermus thermophilus.
[9]
PubMed ID9586030
JournalNucleic Acids Symp Ser
Year1997
Volume(37)
Pages123-4
AuthorsNameki N, Tamura K, Asahara H, Hasegawa T
TitleRecognition of tRNA(Gly) by three widely diverged glycyl-tRNA synthetases: evolution of tRNA recognition.
[10]
CommentsX-ray crystallography
PubMed ID10064708
JournalJ Mol Biol
Year1999
Volume286
Pages1449-59
AuthorsArnez JG, Dock-Bregeon AC, Moras D
TitleGlycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine.
Related PDB1b76,1ggm
[11]
PubMed ID11172710
JournalMol Cell
Year2001
Volume7
Pages43-54
AuthorsCarrodeguas JA, Theis K, Bogenhagen DF, Kisker C
TitleCrystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.
[12]
PubMed ID11485800
JournalTrends Genet
Year2001
Volume17
Pages431-3
AuthorsWolf YI, Koonin EV
TitleOrigin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group.

comments
This enzyme belongs to the class-II aminoacyl-tRNA synthetase family.
Although the tertiary structures with magnesium ions have not been determined yet, each subunit may bind three Mg2+ ions according to the paper [10].
According to the literature [6], [7] and [10], this enzyme catalyzes two successive transfer reactions. Firstly, it transfers the adenylate from ATP (the first substrate) to the carboxylate of the second substrate, glycine, resulting in the formation of glycyl-adenylate (intermediate) and the release of the inorganic pyrophosphate. Secondly, it transfers the acyl group from the intermediate to the 3'-OH of tRNA(Gly).
The first transfer reaction proceeds as follows (see [10]):
(1) The first substrate, ATP, adopts a bent conformation so that the alpha-phosphate group faces the carboxylate of the glycine.
(2) Arg220 stabilizes the negatively charged groups, the acceptor group (the carboxylate) and the transferred group (apha-phosphate of ATP), by neutralizing the charged groups. A magnesium ion coordinated to Glu304 also stabilizes the transferred group, the alpha-phosphate moiety, and the leaving group, the beta-phosphate group.
(3) The stabilization of the negatively charged groups leads to an in-line nucleophilic attack by the carboxylate group on the alpha-phosphorus atom, by associative mechanism (SN2-like mechanism).
(4) The pentacovalent transition state is stabilized by three arginine residues (Arg220, Arg231 & Arg336), and three magnesium ions. Here, the leaving group, the pyrophosphate, is stabilized by two bridging magnesium ions, Arg231 and Arg366.
(5) The leaving group, the inorganic pyrophosphate, leaves the active site, together with the two bridging magnesium ions.
The second acyl transfer reaction has not been elucidated yet.

createdupdated
2004-08-012009-02-26


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