› 6kev

X-ray diffraction
2.51Å resolution

Reduced phosphoribulokinase from Synechococcus elongatus PCC 7942 complexed with adenosine diphosphate and glucose 6-phosphate

Released:
DOI: 10.2210/pdb6kev/pdb
PDB entry 6kev coloured by chain, front view.
PDB entry 6kev coloured by chain, side view.
PDB entry 6kev coloured by chain, top view.
Source organism: Synechococcus elongatus PCC 7942 = FACHB-805
Primary publication:
Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle.
Yu A, Xie Y, Pan X, Zhang H, Cao P, Su X, Chang W, Li M
Plant Cell 32 1556-1573 (2020)
PMID: 32102842

Function and Biology Details

Reaction catalysed: 
ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174271 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphoribulokinase Chain: A
Molecule details ›
Chain: A
Length: 343 amino acids
Theoretical weight: 39.02 KDa
Source organism: Synechococcus elongatus PCC 7942 = FACHB-805
Expression system: Escherichia coli
UniProt:
  • Canonical: Q31PL2 (Residues: 1-333; Coverage: 100%)
Gene name: Synpcc7942_0977
Sequence domains: Phosphoribulokinase / Uridine kinase family

Ligands and Environments

3 bound ligands:
Ligand ADP 1 x ADP
Ligand G6P 1 x G6P
Ligand DTT 1 x DTT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Unit cell:
a: 46.415Å b: 77.104Å c: 94.405Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.19 0.223
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism.
Zhang et al. (2021)
7 more

2 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)
1 more