› 5i93

X-ray diffraction
2.24Å resolution

Structure of Mouse Acireductone dioxygenase with Ni2+ and 2-ketopentanoic acid in the active site

Released:
DOI: 10.2210/pdb5i93/pdb
PDB entry 5i93 coloured by chain, front view.
PDB entry 5i93 coloured by chain, side view.
PDB entry 5i93 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Metal-Dependent Function of a Mammalian Acireductone Dioxygenase.
Deshpande AR, Wagenpfeil K, Pochapsky TC, Petsko GA, Ringe D
Biochemistry 55 1398-407 (2016)
PMID: 26858196

Function and Biology Details

Reactions catalysed: 
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O(2) = 3-(methylthio)propanoate + formate + CO
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O(2) = 4-(methylthio)-2-oxobutanoate + formate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189331 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Acireductone dioxygenase Chain: A
Molecule details ›
Chain: A
Length: 179 amino acids
Theoretical weight: 21.55 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99JT9 (Residues: 1-179; Coverage: 100%)
Gene names: Adi1, Mtcbp1
Sequence domains: ARD/ARD' family
Structure domains: Jelly Rolls

Ligands and Environments

2 bound ligands:
Ligand NI 1 x NI
Ligand 69O 1 x 69O
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P41212
Unit cell:
a: 79.025Å b: 79.025Å c: 115.36Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.18 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Structure, function, and biosynthesis of nickel-dependent enzymes.
Alfano et al. (2020)
3 more