› 2azn

X-ray diffraction
2.7Å resolution

X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase

Released:
DOI: 10.2210/pdb2azn/pdb
PDB entry 2azn coloured by chain, front view.
PDB entry 2azn coloured by chain, side view.
PDB entry 2azn coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Biosynthesis of riboflavin: structure and properties of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase of Methanocaldococcus jannaschii.
Chatwell L, Krojer T, Fidler A, Römisch W, Eisenreich W, Bacher A, Huber R, Fischer M
J Mol Biol 359 1334-51 (2006)
PMID: 16730025

Function and Biology Details

Reaction catalysed: 
2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one + NAD(P)(+) = 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-176557 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 219 amino acids
Theoretical weight: 24.72 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58085 (Residues: 6-224; Coverage: 98%)
Gene names: MJ0671, arfC
Sequence domains: RibD C-terminal domain
Structure domains: Dihydrofolate Reductase, subunit A

Ligands and Environments


Cofactor: Ligand NAP 6 x NAP
2 bound ligands:
Ligand MA5 8 x MA5
Ligand EPE 2 x EPE
1 modified residue:
Ligand MSE 30 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P43212
Unit cell:
a: 137.171Å b: 137.171Å c: 213.87Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.253
Expression system: Escherichia coli

Quick links

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

2 mentions without citation

Structural and functional insights into Saccharomyces cerevisiae riboflavin biosynthesis reductase RIB7.
Lv et al. (2013)
1 more