› 4whp

X-ray diffraction
1.54Å resolution

Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5

Released:
DOI: 10.2210/pdb4whp/pdb
PDB entry 4whp coloured by chain, front view.
PDB entry 4whp coloured by chain, side view.
PDB entry 4whp coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.
Knoot CJ, Purpero VM, Lipscomb JD
Proc Natl Acad Sci U S A 112 388-93 (2015)
PMID: 25548185

Function and Biology Details

Reaction catalysed: 
3,4-dihydroxybenzoate + O(2) = 3-carboxy-cis,cis-muconate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132483 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Protocatechuate 3,4-dioxygenase alpha chain Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 200 amino acids
Theoretical weight: 22.28 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00436 (Residues: 2-201; Coverage: 100%)
Gene name: pcaG
Sequence domains: Dioxygenase
Structure domains: Aromatic compound dioxygenase
Protocatechuate 3,4-dioxygenase beta chain Chains: D, F
Molecule details ›
Chains: D, F
Length: 238 amino acids
Theoretical weight: 26.7 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00437 (Residues: 2-239; Coverage: 100%)
Gene name: pcaH
Sequence domains:
Structure domains: Aromatic compound dioxygenase
Protocatechuate 3,4-dioxygenase beta chain Chain: B
Molecule details ›
Chain: B
Length: 238 amino acids
Theoretical weight: 26.71 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00437 (Residues: 2-239; Coverage: 100%)
Gene name: pcaH
Sequence domains:
Structure domains: Aromatic compound dioxygenase

Ligands and Environments

4 bound ligands:
Ligand FE 3 x FE
Ligand SO4 3 x SO4
Ligand BCT 1 x BCT
Ligand BME 1 x BME
1 modified residue:
Ligand MHO 1 x MHO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I222
Unit cell:
a: 127.919Å b: 140.767Å c: 168.191Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.142 0.14 0.172
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics.
Wang et al. (2017)
1 more

1 mention without citation

Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.
Knoot et al. (2015)