› 3ukd

X-ray diffraction
1.9Å resolution

UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP, AND ALF3

Released:
DOI: 10.2210/pdb3ukd/pdb
PDB entry 3ukd coloured by chain, front view.
PDB entry 3ukd coloured by chain, side view.
PDB entry 3ukd coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
Schlichting I, Reinstein J
Biochemistry 36 9290-6 (1997)
PMID: 9280438

Function and Biology Details

Reaction catalysed: 
ATP + (d)CMP = ADP + (d)CDP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148970 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UMP-CMP kinase Chain: A
Molecule details ›
Chain: A
Length: 194 amino acids
Theoretical weight: 21.97 KDa
Source organism: Dictyostelium discoideum
Expression system: Escherichia coli
UniProt:
  • Canonical: P20425 (Residues: 2-195; Coverage: 100%)
Gene names: DDB_G0287495, ctpS, pyrK
Sequence domains: Adenylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand ADP 1 x ADP
Ligand C5P 1 x C5P
Ligand AF3 1 x AF3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P41212
Unit cell:
a: 78.8Å b: 78.8Å c: 100.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.198 0.232
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The catalytic mechanism of nucleoside diphosphate kinases.
Lascu et al. (2000)
6 more

3 mentions without citation

Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction.
Zeymer et al. (2016)
2 more