› 4aq6

X-ray diffraction
1.98Å resolution

substrate bound homogentisate 1,2-dioxygenase

Released:
DOI: 10.2210/pdb4aq6/pdb
PDB entry 4aq6 coloured by chain, front view.
PDB entry 4aq6 coloured by chain, side view.
PDB entry 4aq6 coloured by chain, top view.
Source organism: Pseudomonas putida KT2440
Primary publication:
Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase.
Jeoung JH, Bommer M, Lin TY, Dobbek H
Proc Natl Acad Sci U S A 110 12625-30 (2013)
PMID: 23858455

Function and Biology Details

Reaction catalysed: 
Homogentisate + O(2) = 4-maleylacetoacetate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183455 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Homogentisate 1,2-dioxygenase Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 433 amino acids
Theoretical weight: 48.06 KDa
Source organism: Pseudomonas putida KT2440
Expression system: Escherichia coli
UniProt:
  • Canonical: Q88E47 (Residues: 1-433; Coverage: 100%)
Gene names: PP_4621, hmgA
Sequence domains:
Structure domains: Jelly Rolls

Ligands and Environments

3 bound ligands:
Ligand FE 12 x FE
Ligand OMD 12 x OMD
Ligand B3P 1 x B3P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P1
Unit cell:
a: 93.393Å b: 93.714Å c: 162.984Å
α: 87.69° β: 80.42° γ: 68.39°
R-values:
R R work R free
0.164 0.161 0.216
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes.
Jasniewski et al. (2018)
5 more

4 mentions without citation

mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance.
Pires et al. (2016)
3 more