› 6fxq

X-ray diffraction
1.69Å resolution

Structure of coproheme decarboxylase from Listeria monocytogenes during turnover

Released:
DOI: 10.2210/pdb6fxq/pdb
PDB entry 6fxq coloured by chain, front view.
PDB entry 6fxq coloured by chain, side view.
PDB entry 6fxq coloured by chain, top view.
Source organism: Listeria monocytogenes EGD-e
Primary publication:
Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b.
Milazzo L, Gabler T, Pühringer D, Jandova Z, Maresch D, Michlits H, Pfanzagl V, Djinović-Carugo K, Oostenbrink C, Furtmüller PG, Obinger C, Smulevich G, Hofbauer S
ACS Catal 9 6766-6782 (2019)
PMID: 31423350

Function and Biology Details

Reaction catalysed: 
(1a) Fe-coproporphyrin III + H(2)O(2) = harderoheme III + CO(2) + 2 H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186958 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Coproheme decarboxylase Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 250 amino acids
Theoretical weight: 28.75 KDa
Source organism: Listeria monocytogenes EGD-e
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8Y5F1 (Residues: 2-251; Coverage: 100%)
Gene names: chdC, hemQ, lmo2113
Sequence domains: Chlorite dismutase

Ligands and Environments

4 bound ligands:
Ligand NA 5 x NA
Ligand FEC 5 x FEC
Ligand VOV 5 x VOV
Ligand MPD 4 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 77.687Å b: 129.369Å c: 77.916Å
α: 90° β: 105.52° γ: 90°
R-values:
R R work R free
0.179 0.178 0.214
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Understanding molecular enzymology of porphyrin-binding α + β barrel proteins - One fold, multiple functions.
Hofbauer et al. (2021)
1 more

4 mentions without citation

Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis.
Falb et al. (2023)
3 more