› 5a88

X-ray diffraction
2.08Å resolution

Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with ADP

Released:
DOI: 10.2210/pdb5a88/pdb
PDB entry 5a88 coloured by chain, front view.
PDB entry 5a88 coloured by chain, side view.
PDB entry 5a88 coloured by chain, top view.
Source organism: Corynebacterium ammoniagenes
Primary publication:
Structural insights into the synthesis of FMN in prokaryotic organisms.
Herguedas B, Lans I, Sebastián M, Hermoso JA, Martínez-Júlvez M, Medina M
Acta Crystallogr D Biol Crystallogr 71 2526-42 (2015)
PMID: 26627660

Function and Biology Details

Reactions catalysed: 
ATP + riboflavin = ADP + FMN
ATP + FMN = diphosphate + FAD
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176786 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional riboflavin kinase/FMN adenylyltransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 156 amino acids
Theoretical weight: 17.14 KDa
Source organism: Corynebacterium ammoniagenes
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q59263 (Residues: 183-338; Coverage: 46%)
Gene name: ribF
Sequence domains: Riboflavin kinase
Structure domains: Riboflavin kinase-like

Ligands and Environments

3 bound ligands:
Ligand ADP 4 x ADP
Ligand GOL 6 x GOL
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P32
Unit cell:
a: 68.664Å b: 68.664Å c: 147.006Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.161 0.159 0.189
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Riboflavin transport and metabolism in humans.
Barile et al. (2016)
2 more

1 mention without citation

Structural Insight into the Working Mechanism of the FAD Synthetase from the Human Pathogen Streptococcus pneumoniae: A Molecular Docking Simulation Study.
Kwon S. (2023)