› 4qgn

X-ray diffraction
3.05Å resolution

Human acireductone dioxygenase with iron ion and L-methionine in active center

Released:
DOI: 10.2210/pdb4qgn/pdb
PDB entry 4qgn coloured by chain, front view.
PDB entry 4qgn coloured by chain, side view.
PDB entry 4qgn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase.
Miłaczewska A, Kot E, Amaya JA, Makris TM, Zając M, Korecki J, Chumakov A, Trzewik B, Kędracka-Krok S, Minor W, Chruszcz M, Borowski T
Chemistry 24 5225-5237 (2018)
PMID: 29193386

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-189752 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Acireductone dioxygenase Chain: A
Molecule details ›
Chain: A
Length: 183 amino acids
Theoretical weight: 21.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BV57 (Residues: 1-179; Coverage: 100%)
Gene names: ADI1, HMFT1638, MTCBP1
Sequence domains: ARD/ARD' family
Structure domains: Jelly Rolls

Ligands and Environments

5 bound ligands:
Ligand FE 1 x FE
Ligand CL 2 x CL
Ligand MSE 1 x MSE
Ligand SO4 4 x SO4
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P64
Unit cell:
a: 105.195Å b: 105.195Å c: 40.822Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.178 0.228
Expression system: Escherichia coli

Quick links

Citations

2 review citations

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

6 mentions without citation

The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase.
Deshpande et al. (2017)
5 more