› 2ip4

X-ray diffraction
2.8Å resolution

Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8

Released:
DOI: 10.2210/pdb2ip4/pdb
PDB entry 2ip4 coloured by chain, front view.
PDB entry 2ip4 coloured by chain, side view.
PDB entry 2ip4 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
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-178061 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphoribosylamine--glycine ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 417 amino acids
Theoretical weight: 44.89 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SK40 (Residues: 1-417; Coverage: 100%)
Gene names: TTHA0812, purD
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand SO4 4 x SO4
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 72.308Å b: 98.068Å c: 121.142Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.218 0.238
Expression system: Escherichia coli

Quick links

Citations

11 citation in other articles

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

2 mentions without citation

Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry.
Wang et al. (2019)
1 more