› 1z42

X-ray diffraction
1.85Å resolution

Crystal structure of oxidized YqjM from Bacillus subtilis complexed with p-hydroxybenzaldehyde

Released:
DOI: 10.2210/pdb1z42/pdb
PDB entry 1z42 coloured by chain, front view.
PDB entry 1z42 coloured by chain, side view.
PDB entry 1z42 coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of Old Yellow Enzymes.
Kitzing K, Fitzpatrick TB, Wilken C, Sawa J, Bourenkov GP, Macheroux P, Clausen T
J Biol Chem 280 27904-13 (2005)
PMID: 15890652

Function and Biology Details

Reaction catalysed: 
NADPH + acceptor = NADP(+) + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157042 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NADPH dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 338 amino acids
Theoretical weight: 38.15 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: P54550 (Residues: 1-338; Coverage: 100%)
Gene names: BSU23820, namA, yqjM
Sequence domains: NADH:flavin oxidoreductase / NADH oxidase family
Structure domains: Aldolase class I

Ligands and Environments


Cofactor: Ligand FMN 2 x FMN
2 bound ligands:
Ligand SO4 2 x SO4
Ligand HBA 2 x HBA
1 modified residue:
Ligand MSE 22 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: C2221
Unit cell:
a: 51.167Å b: 184.681Å c: 169.172Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.182 0.204
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Microbial 2,4,6-trinitrotoluene degradation: could we learn from (bio)chemistry for bioremediation and vice versa?
Stenuit et al. (2010)
1 more

1 mention without citation

Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences.
Nizam et al. (2014)