› 4pgi

X-ray diffraction
2.08Å resolution

Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound

Released:
DOI: 10.2210/pdb4pgi/pdb
PDB entry 4pgi coloured by chain, front view.
PDB entry 4pgi coloured by chain, side view.
PDB entry 4pgi coloured by chain, top view.
Source organism: Prochlorococcus marinus str. MIT 9313
Primary publication:
Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound.
Buer BC, Paul B, Das D, Stuckey JA, Marsh EN
ACS Chem Biol 9 2584-93 (2014)
PMID: 25222710

Function and Biology Details

Reaction catalysed: 
A long-chain aldehyde + O(2) + 2 NADPH = an alkane + formate + H(2)O + 2 NADP(+)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182056 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aldehyde decarbonylase Chain: A
Molecule details ›
Chain: A
Length: 250 amino acids
Theoretical weight: 28.05 KDa
Source organism: Prochlorococcus marinus str. MIT 9313
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7V6D4 (Residues: 1-243; Coverage: 100%)
Gene name: PMT_1231
Sequence domains: Long-chain fatty aldehyde decarbonylase
Structure domains: Ferritin

Ligands and Environments

3 bound ligands:
Ligand FE 2 x FE
Ligand Y69 1 x Y69
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P43212
Unit cell:
a: 77.071Å b: 77.071Å c: 117.259Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.222
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Enzymes for fatty acid-based hydrocarbon biosynthesis.
Herman et al. (2016)
1 more

5 mentions without citation

Recent advances in the improvement of cyanobacterial enzymes for bioalkane production.
Hayashi et al. (2022)
4 more