› 2obc

X-ray diffraction
3Å resolution

The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain

Released:
DOI: 10.2210/pdb2obc/pdb
PDB entry 2obc coloured by chain, front view.
PDB entry 2obc coloured by chain, side view.
PDB entry 2obc 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-150500 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Riboflavin biosynthesis protein RibD Chains: A, B
Molecule details ›
Chains: A, B
Length: 402 amino acids
Theoretical weight: 44.8 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P25539 (Residues: 2-367; Coverage: 100%)
Gene names: JW0404, b0414, ribD, ribG, ybaE
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand RP5 1 x RP5
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P3121
Unit cell:
a: 173.1Å b: 173.1Å c: 76.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.222 0.276
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers.
Abbas et al. (2011)
3 more

4 mentions without citation

Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance.
Cheng et al. (2016)
3 more