› 2vbv

X-ray diffraction
2.4Å resolution

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN

Released:
DOI: 10.2210/pdb2vbv/pdb
PDB entry 2vbv coloured by chain, front view.
PDB entry 2vbv coloured by chain, side view.
PDB entry 2vbv coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.
Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M
Structure 15 1577-90 (2007)
PMID: 18073108

Function and Biology Details

Reaction catalysed: 
CTP + riboflavin = CDP + FMN
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178777 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Riboflavin kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 136 amino acids
Theoretical weight: 15.71 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q60365 (Residues: 1-132; Coverage: 100%)
Gene names: MJ0056, ribK
Sequence domains: Domain of unknown function DUF120
Structure domains: Riboflavin kinase-like

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN
4 bound ligands:
Ligand CDP 2 x CDP
Ligand MG 2 x MG
Ligand IOD 1 x IOD
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 41.482Å b: 73.299Å c: 104.907Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.227 0.323
Expression system: Escherichia coli

Quick links

Citations

2 review citations

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

1 mention without citation

A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.
Rodionova et al. (2017)