› 6cty

X-ray diffraction
2.41Å resolution

Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution

Released:
DOI: 10.2210/pdb6cty/pdb
PDB entry 6cty coloured by chain, front view.
PDB entry 6cty coloured by chain, side view.
PDB entry 6cty coloured by chain, top view.
Source organism: Yersinia pestis
Primary publication:
Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.
Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W
Int J Biol Macromol 136 1176-1187 (2019)
PMID: 31207330

Function and Biology Details

Reaction catalysed: 
(S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187197 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydroorotase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 372 amino acids
Theoretical weight: 41.41 KDa
Source organism: Yersinia pestis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8ZFU4 (Residues: 1-348; Coverage: 100%)
Gene names: YPO1587, YP_2265, pyrC, y1746
Sequence domains: Amidohydrolase family
Structure domains: Metal-dependent hydrolases

Ligands and Environments

2 bound ligands:
Ligand ZN 12 x ZN
Ligand MLT 5 x MLT
2 modified residues:
Ligand KCX 6 x KCX
Ligand CSX 12 x CSX

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 95.838Å b: 112.202Å c: 208.264Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.159 0.198
Expression system: Escherichia coli BL21

Quick links

Citations

9 citation in other articles

Complexed Crystal Structure of Saccharomyces cerevisiae Dihydroorotase with Inhibitor 5-Fluoroorotate Reveals a New Binding Mode.
Guan et al. (2021)
8 more

2 mentions without citation

Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.
Lipowska et al. (2019)
1 more