› 2ys6

X-ray diffraction
2.21Å resolution

Crystal structure of GAR synthetase from Geobacillus kaustophilus

Released:
DOI: 10.2210/pdb2ys6/pdb
PDB entry 2ys6 coloured by chain, front view.
PDB entry 2ys6 coloured by chain, side view.
PDB entry 2ys6 coloured by chain, top view.
Source organism: Geobacillus kaustophilus
Primary publication:
Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria.
Sampei G, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G
J Biochem 148 429-38 (2010)
PMID: 20716513

Function and Biology Details

Reaction catalysed: 
ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177419 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphoribosylamine--glycine ligase Chain: A
Molecule details ›
Chain: A
Length: 451 amino acids
Theoretical weight: 48.23 KDa
Source organism: Geobacillus kaustophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5L3C7 (Residues: 1-430; Coverage: 100%)
Gene names: GK0268, purD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GLY 1 x GLY
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P212121
Unit cell:
a: 50.786Å b: 83.43Å c: 96.536Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.23
Expression system: Escherichia coli

Quick links

Citations

10 citation in other articles

Helicobacter pylori relies primarily on the purine salvage pathway for purine nucleotide biosynthesis.
Liechti et al. (2012)
9 more

3 mentions without citation

Structural biology of the purine biosynthetic pathway.
Zhang et al. (2008)
2 more