› 1dio

X-ray diffraction
2.2Å resolution

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

Released:
DOI: 10.2210/pdb1dio/pdb
PDB entry 1dio coloured by chain, front view.
PDB entry 1dio coloured by chain, side view.
PDB entry 1dio coloured by chain, top view.
Source organism: Klebsiella oxytoca
Primary publication:
A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Shibata N, Masuda J, Tobimatsu T, Toraya T, Suto K, Morimoto Y, Yasuoka N
Structure 7 997-1008 (1999)
PMID: 10467140

Function and Biology Details

Reaction catalysed: 
Propane-1,2-diol = propanal + H(2)O
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-176799 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Diol/glycerol dehydratase large subunit domain-containing protein Chains: A, L
Molecule details ›
Chains: A, L
Length: 554 amino acids
Theoretical weight: 60.41 KDa
Source organism: Klebsiella oxytoca
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59470 (Residues: 1-554; Coverage: 100%)
Gene names: AI3012V1_3144, F6W21_13300, pddA, pduC
Sequence domains: Dehydratase large subunit
Structure domains: Diol/glycerol dehydratase, large subunit
Diol dehydrase beta subunit Chains: B, E
Molecule details ›
Chains: B, E
Length: 224 amino acids
Theoretical weight: 24.14 KDa
Source organism: Klebsiella oxytoca
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59471 (Residues: 1-224; Coverage: 100%)
Gene name: pddB
Sequence domains: Dehydratase medium subunit
Structure domains: B12-dependent dehydatase associated subunit
Diol dehydrase gamma subunit Chains: G, M
Molecule details ›
Chains: G, M
Length: 173 amino acids
Theoretical weight: 19.2 KDa
Source organism: Klebsiella oxytoca
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59472 (Residues: 1-173; Coverage: 100%)
Gene name: pddC
Sequence domains: Dehydratase small subunit
Structure domains: Propanediol/glycerol dehydratase, small subunit

Ligands and Environments


Cofactor: Ligand B12 2 x B12
2 bound ligands:
Ligand K 2 x K
Ligand PGO 2 x PGO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 76.2Å b: 122.3Å c: 209.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.187 0.236
Expression system: Escherichia coli

Quick links

Citations

23 review citations

The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes.
Banerjee et al. (2003)
22 more

7 mentions without citation

Molecular Mechanisms of Enzyme Activation by Monovalent Cations.
Gohara et al. (2016)
6 more