› 1pvy

X-ray diffraction
1.7Å resolution

3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate

Released:
DOI: 10.2210/pdb1pvy/pdb
PDB entry 1pvy coloured by chain, front view.
PDB entry 1pvy coloured by chain, side view.
PDB entry 1pvy coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.
Steinbacher S, Schiffmann S, Richter G, Huber R, Bacher A, Fischer M
J Biol Chem 278 42256-65 (2003)
PMID: 12904291

Function and Biology Details

Reaction catalysed: 
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178775 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3,4-dihydroxy-2-butanone 4-phosphate synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 227 amino acids
Theoretical weight: 25.78 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q60364 (Residues: 1-227; Coverage: 100%)
Gene names: MJ0055, ribB
Sequence domains: 3,4-dihydroxy-2-butanone 4-phosphate synthase
Structure domains: DHBP synthase

Ligands and Environments

3 bound ligands:
Ligand 5RP 2 x 5RP
Ligand ZN 3 x ZN
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21
Unit cell:
a: 53.197Å b: 69.272Å c: 57.11Å
α: 90° β: 93.52° γ: 90°
R-values:
R R work R free
0.223 0.213 0.259
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers.
Abbas et al. (2011)
2 more

2 mentions without citation

Predicting the disruption by UO2(2+) of a protein-ligand interaction.
Pible et al. (2010)
1 more