› 2o7p

X-ray diffraction
3Å resolution

The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain

Released:
DOI: 10.2210/pdb2o7p/pdb
PDB entry 2o7p coloured by chain, front view.
PDB entry 2o7p coloured by chain, side view.
PDB entry 2o7p coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism.
Stenmark P, Moche M, Gurmu D, Nordlund P
J Mol Biol 373 48-64 (2007)
PMID: 17765262

Function and Biology Details

Reactions catalysed: 
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5-phosphoribosylamino)uracil + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174919 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Riboflavin biosynthesis protein RibD Chains: A, B
Molecule details ›
Chains: A, B
Length: 380 amino acids
Theoretical weight: 42.37 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q3ZUB0 (Residues: 2-367; Coverage: 100%)
Gene names: ACU57_11920, BANRA_03616, BGM66_000476, BJI68_13990, CTR35_002873, E4K51_12185, EIZ93_00945, FOI11_011390, FOI11_08655, FWK02_17570, G3V95_13340, GNW61_04815, GRW05_11885, GRW57_05470, HMV95_11685, J0541_001726, JNP96_06500, NCTC9117_04777, ribD
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAP 2 x NAP
No bound ligands
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P3121
Unit cell:
a: 173Å b: 173Å c: 77.8Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.212 0.267
Expression system: Escherichia coli BL21(DE3)

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

4 mentions without citation

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs.
Islam et al. (2023)
3 more