› 2bmu

X-ray diffraction
2.55Å resolution

UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE UMP AND ITS SUBSTRATE ANALOG AMPPNP

Released:
DOI: 10.2210/pdb2bmu/pdb
PDB entry 2bmu coloured by chain, front view.
PDB entry 2bmu coloured by chain, side view.
PDB entry 2bmu coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis.
Marco-Marín C, Gil-Ortiz F, Rubio V
J Mol Biol 352 438-54 (2005)
PMID: 16095620

Function and Biology Details

Reaction catalysed: 
ATP + UMP = ADP + UDP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186384 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 226 amino acids
Theoretical weight: 24.78 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8U122 (Residues: 1-225; Coverage: 100%)
Gene names: PF1407, pyrH
Sequence domains: Amino acid kinase family
Structure domains: Acetylglutamate kinase-like

Ligands and Environments

3 bound ligands:
Ligand ANP 2 x ANP
Ligand U5P 2 x U5P
Ligand MG 4 x MG
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: I23
Unit cell:
a: 144.564Å b: 144.564Å c: 144.564Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.191 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

The N-Acetylglutamate Synthase Family: Structures, Function and Mechanisms.
Shi et al. (2015)
1 more

5 mentions without citation

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance.
Hove-Jensen et al. (2017)
4 more