DB code: D00295

RLCP classification 3.113.90030.2130 : Transfer
CATH domain 3.30.930.10 : BirA Bifunctional Protein; domain 2 Catalytic domain
3.40.50.800 : Rossmann fold
E.C. 6.1.1.14
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P56206 Glycyl-tRNA synthetase
EC 6.1.1.14
Glycine--tRNA ligase
GlyRS
YP_143809.1 (Protein)
NC_006461.1 (DNA/RNA sequence)
PF03129 (HGTP_anticodon)
PF00587 (tRNA-synt_2b)
[Graphical View]

KEGG enzyme name
glycine---tRNA ligase
glycyl-tRNA synthetase
glycyl-transfer ribonucleate synthetase
glycyl-transfer RNA synthetase
glycyl-transfer ribonucleic acid synthetase
glycyl translase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P56206 SYG_THET8 ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly). Homodimer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00260 Glycine, serine and threonine metabolism
MAP00970 Aminoacyl-tRNA biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00037 C01642 C00020 C00013 C02412
E.C.
Compound Magnesium ATP Glycine tRNA(Gly) AMP Pyrophosphate Glycyl-tRNA(Gly) Glycyl-adenylate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids nucleic acids amine group,nucleotide phosphate group/phosphate ion amino acids,nucleic acids
ChEBI 18420
 18420
 		15422
 15422
 		15428
 57305
 15428
 57305
 		16027
 16027
 		29888
 29888
PubChem 888
 888
 		5957
 5957
 		5257127
 750
 5257127
 750
 		6083
 6083
 		1023
 21961011
 1023
 21961011
1atiA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1atiB01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b76A01 Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound
1b76B01 Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound
1ggmA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:GAP
1ggmB01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:GAP
1atiA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1atiB02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b76A02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b76B02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ggmA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ggmB02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [7] & [10]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1atiA01 ARG 220;ARG 231;ARG 366 ASP 293;GLU 304(magnesium binding)
1atiB01 ARG 220;ARG 231;ARG 366 ASP 293;GLU 304(magnesium binding)
1b76A01 ARG 220;ARG 231;ARG 366 ASP 293;GLU 304(magnesium binding)
1b76B01 ARG 220;ARG 231;ARG 366 ASP 293;GLU 304(magnesium binding)
1ggmA01 ARG 220;ARG 231;ARG 366 ASP 293;GLU 304(magnesium binding)
1ggmB01 ARG 220;ARG 231;ARG 366 ASP 293;GLU 304(magnesium binding)
1atiA02
1atiB02
1b76A02
1b76B02
1ggmA02
1ggmB02

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
p.4158
[7]
p.346-348
[10]
Fig.5, p.1455 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 6262123
Journal FEBS Lett
Year 1981
Volume 124
Pages 293-8
Authors Led JJ, Andersen AJ
Title The use of paramagnetic 13C NMR relaxation to study the mechanisms of the amino acid activation catalysed by a cognate tRNA synthetase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6315429
Journal Eur J Biochem
Year 1983
Volume 136
Pages 469-79
Authors Led JJ, Switon WK, Jensen KF
Title Phosphorolytic activity of Escherichia coli glycyl-tRNA synthetase towards its cognate aminoacyl adenylate detected by 31P-NMR spectroscopy and thin-layer chromatography.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1546312
Journal Science
Year 1992
Volume 255
Pages 1121-5
Authors Francklyn C, Shi JP, Schimmel P
Title Overlapping nucleotide determinants for specific aminoacylation of RNA microhelices.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8071996
Journal J Mol Biol
Year 1994
Volume 241
Pages 732-5
Authors Logan DT, Cura V, Touzel JP, Kern D, Moras D
Title Crystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and initial crystallographic data.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8845358
Journal Biochemistry
Year 1995
Volume 34
Pages 16327-36
Authors Wu H, Nada S, Dignam JD
Title Analysis of truncated forms of Bombyx mori glycyl-tRNA synthetase: function of an N-terminal structure in RNA binding.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 7556056
Journal EMBO J
Year 1995
Volume 14
Pages 4156-67
Authors Logan DT, Mazauric MH, Kern D, Moras D
Title Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus.
Related PDB 1ati
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8839980
Journal Biol Chem Hoppe Seyler
Year 1996
Volume 377
Pages 343-56
Authors Freist W, Logan DT, Gauss DH
Title Glycyl-tRNA synthetase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8944770
Journal Eur J Biochem
Year 1996
Volume 241
Pages 814-26
Authors Mazauric MH, Reinbolt J, Lorber B, Ebel C, Keith G, Giege R, Kern D
Title An example of non-conservation of oligomeric structure in prokaryotic aminoacyl-tRNA synthetases. Biochemical and structural properties of glycyl-tRNA synthetase from Thermus thermophilus.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9586030
Journal Nucleic Acids Symp Ser
Year 1997
Volume (37)
Pages 123-4
Authors Nameki N, Tamura K, Asahara H, Hasegawa T
Title Recognition of tRNA(Gly) by three widely diverged glycyl-tRNA synthetases: evolution of tRNA recognition.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10064708
Journal J Mol Biol
Year 1999
Volume 286
Pages 1449-59
Authors Arnez JG, Dock-Bregeon AC, Moras D
Title Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine.
Related PDB 1b76 1ggm
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11172710
Journal Mol Cell
Year 2001
Volume 7
Pages 43-54
Authors Carrodeguas JA, Theis K, Bogenhagen DF, Kisker C
Title Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11485800
Journal Trends Genet
Year 2001
Volume 17
Pages 431-3
Authors Wolf YI, Koonin EV
Title Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group.
Related PDB
Related UniProtKB

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.

Created Updated
2004-08-01 2009-02-26