› 2dua

X-ray diffraction
2Å resolution

Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++

Released:
DOI: 10.2210/pdb2dua/pdb
PDB entry 2dua coloured by chain, front view.
PDB entry 2dua coloured by chain, side view.
PDB entry 2dua coloured by chain, top view.
Source organism: Variovorax sp. Pal2
Primary publication:
Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily.
Chen CC, Han Y, Niu W, Kulakova AN, Howard A, Quinn JP, Dunaway-Mariano D, Herzberg O
Biochemistry 45 11491-504 (2006)
PMID: 16981709

Function and Biology Details

Reaction catalysed: 
3-phosphonopyruvate + H(2)O = pyruvate + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183037 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphonopyruvate hydrolase Chain: A
Molecule details ›
Chain: A
Length: 290 amino acids
Theoretical weight: 31.22 KDa
Source organism: Variovorax sp. Pal2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q84G06 (Residues: 1-290; Coverage: 100%)
Gene names: palA, pphA
Sequence domains: Phosphoenolpyruvate phosphomutase
Structure domains: Phosphoenolpyruvate-binding domains

Ligands and Environments

5 bound ligands:
Ligand XYS 1 x XYS
Ligand OXL 1 x OXL
Ligand MG 1 x MG
Ligand NA 1 x NA
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-BM
Spacegroup: I222
Unit cell:
a: 74.89Å b: 79.18Å c: 93.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.156 0.219
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

New ways to break an old bond: the bacterial carbon-phosphorus hydrolases and their role in biogeochemical phosphorus cycling.
Quinn et al. (2007)
4 more

1 mention without citation

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships.
Lo et al. (2008)