› 5b3f

X-ray diffraction
2.5Å resolution

Crystal structure of phosphoribulokinase from Methanospirillum hungatei

Released:
DOI: 10.2210/pdb5b3f/pdb
PDB entry 5b3f coloured by chain, front view.
PDB entry 5b3f coloured by chain, side view.
PDB entry 5b3f coloured by chain, top view.
Source organism: Methanospirillum hungatei JF-1
Primary publication:
A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea.
Kono T, Mehrotra S, Endo C, Kizu N, Matusda M, Kimura H, Mizohata E, Inoue T, Hasunuma T, Yokota A, Matsumura H, Ashida H
Nat Commun 8 14007 (2017)
PMID: 28082747

Function and Biology Details

Reaction catalysed: 
ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173407 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
phosphoribulokinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 343 amino acids
Theoretical weight: 39.68 KDa
Source organism: Methanospirillum hungatei JF-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q2FUB5 (Residues: 1-323; Coverage: 100%)
Gene name: Mhun_0794
Sequence domains: Phosphoribulokinase / Uridine kinase family

Ligands and Environments

1 bound ligand:
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 78.414Å b: 93.822Å c: 99.942Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.223 0.279
Expression system: Escherichia coli

Quick links

Citations

8 review citations

A physiological perspective on the origin and evolution of photosynthesis.
Martin et al. (2018)
7 more

4 mentions without citation

Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate.
Meloni et al. (2023)
3 more