› 1kol

X-ray diffraction
1.65Å resolution

Crystal structure of formaldehyde dehydrogenase

Released:
DOI: 10.2210/pdb1kol/pdb
PDB entry 1kol coloured by chain, front view.
PDB entry 1kol coloured by chain, side view.
PDB entry 1kol coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases.
Tanaka N, Kusakabe Y, Ito K, Yoshimoto T, Nakamura KT
J Mol Biol 324 519-33 (2002)
PMID: 12445786

Function and Biology Details

Reactions catalysed: 
Formaldehyde + NAD(+) + H(2)O = formate + NADH
2 formaldehyde + H(2)O = formate + methanol
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155444 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glutathione-independent formaldehyde dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 398 amino acids
Theoretical weight: 41.99 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli
UniProt:
  • Canonical: P46154 (Residues: 2-399; Coverage: 100%)
Gene name: fdhA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
2 bound ligands:
Ligand ZN 4 x ZN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P3112
Unit cell:
a: 85.686Å b: 85.686Å c: 190.752Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.171 0.206
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily.
Persson et al. (2008)
2 more

7 mentions without citation

ECOD: an evolutionary classification of protein domains.
Cheng et al. (2014)
6 more