› 1yki

X-ray diffraction
1.7Å resolution

The structure of E. coli nitroreductase bound with the antibiotic nitrofurazone

Released:
DOI: 10.2210/pdb1yki/pdb
PDB entry 1yki coloured by chain, front view.
PDB entry 1yki coloured by chain, side view.
PDB entry 1yki coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme.
Race PR, Lovering AL, Green RM, Ossor A, White SA, Searle PF, Wrighton CJ, Hyde EI
J Biol Chem 280 13256-64 (2005)
PMID: 15684426

Function and Biology Details

Reaction catalysed: 
A 5,6,7,8-tetrahydropteridine + NAD(P)(+) = a 6,7-dihydropteridine + NAD(P)H
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-153657 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oxygen-insensitive NAD(P)H nitroreductase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 217 amino acids
Theoretical weight: 23.94 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P38489 (Residues: 1-217; Coverage: 100%)
Gene names: JW0567, b0578, dprA, nfnB, nfsB, nfsI, ntr
Sequence domains: Nitroreductase family
Structure domains: NADH Oxidase

Ligands and Environments


Cofactor: Ligand FMN 4 x FMN
3 bound ligands:
Ligand NFZ 4 x NFZ
Ligand DMS 3 x DMS
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 70.078Å b: 56.466Å c: 116.085Å
α: 90° β: 103.1° γ: 90°
R-values:
R R work R free
0.145 0.144 0.167
Expression system: Escherichia coli BL21

Quick links

Citations

6 review citations

Reduction of polynitroaromatic compounds: the bacterial nitroreductases.
Roldán et al. (2008)
5 more

11 mentions without citation

The distribution and mechanism of iodotyrosine deiodinase defied expectations.
Sun et al. (2017)
10 more