› 5yfu

X-ray diffraction
2.35Å resolution

Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate and AMP

Released:
DOI: 10.2210/pdb5yfu/pdb
PDB entry 5yfu coloured by chain, front view.
PDB entry 5yfu coloured by chain, side view.
PDB entry 5yfu coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.
Gogoi P, Kanaujia SP
Sci Rep 8 1891 (2018)
PMID: 29382938

Function and Biology Details

Reaction catalysed: 
Alpha-D-ribose 1,5-bisphosphate = D-ribulose 1,5-bisphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129642 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribose 1,5-bisphosphate isomerase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 324 amino acids
Theoretical weight: 36.46 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O57947 (Residues: 1-324; Coverage: 100%)
Gene name: PH0208
Sequence domains: Initiation factor 2 subunit family
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand RUB 3 x RUB
Ligand K 3 x K
Ligand AMP 3 x AMP
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P3112
Unit cell:
a: 98.98Å b: 98.98Å c: 256.611Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.184 0.18 0.248
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.
Hove-Jensen et al. (2019)
2 other articles

2 mentions without citation

A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.
Gogoi et al. (2018)
1 more