› 3mbi

X-ray diffraction
1.8Å resolution

Crystal structure of the phosphoribosylpyrophosphate (PRPP) synthetase from Thermoplasma volcanium in complex with ADP-Mg2+ and ribose 5-phosphate

Released:
DOI: 10.2210/pdb3mbi/pdb
PDB entry 3mbi coloured by chain, front view.
PDB entry 3mbi coloured by chain, side view.
PDB entry 3mbi coloured by chain, top view.
Source organism: Thermoplasma volcanium
Primary publication:
The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs.
Cherney MM, Cherney LT, Garen CR, James MN
J Mol Biol 413 844-56 (2011)
PMID: 21963988

Function and Biology Details

Reaction catalysed: 
ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-572720 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribose-phosphate pyrophosphokinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 287 amino acids
Theoretical weight: 32.29 KDa
Source organism: Thermoplasma volcanium
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97CA5 (Residues: 1-285; Coverage: 100%)
Gene names: TV0197, TVG0201915, prs
Sequence domains:
Structure domains: Rossmann fold

Ligands and Environments

4 bound ligands:
Ligand PO4 3 x PO4
Ligand MG 4 x MG
Ligand ADP 4 x ADP
Ligand HSX 1 x HSX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 76.599Å b: 61.841Å c: 127.938Å
α: 90° β: 103.94° γ: 90°
R-values:
R R work R free
0.178 0.176 0.219
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being.
Ugbogu et al. (2022)
4 other articles

5 mentions without citation

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance.
Hove-Jensen et al. (2017)
4 more