› 4c8r

X-ray diffraction
2.82Å resolution

Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(II) and N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine (AR692B)

Released:
DOI: 10.2210/pdb4c8r/pdb
PDB entry 4c8r coloured by chain, front view.
PDB entry 4c8r coloured by chain, side view.
PDB entry 4c8r coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Modulating carnitine levels by targeting its biosynthesis pathway - selective inhibition of γ-butyrobetaine hydroxylase.
Rydzik AM, Chowdhury R, Kochan GT, Williams ST, McDonough MA, Kawamura A, Schofield CJ
Chem Sci 5 1765-1771 (2014)
PMID: 26682037

Function and Biology Details

Reaction catalysed: 
4-trimethylammoniobutanoate + 2-oxoglutarate + O(2) = 3-hydroxy-4-trimethylammoniobutanoate + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131180 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Gamma-butyrobetaine dioxygenase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 388 amino acids
Theoretical weight: 44.86 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O75936 (Residues: 1-387; Coverage: 100%)
Gene names: BBH, BBOX, BBOX1
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand NI 6 x NI
Ligand ZN 6 x ZN
Ligand 6YT 6 x 6YT
Ligand EDO 14 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 195.744Å b: 91.659Å c: 167.132Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.244
Expression system: Trichoplusia ni

Quick links

Citations

2 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
1 more

2 mentions without citation

Modulating carnitine levels by targeting its biosynthesis pathway - selective inhibition of γ-butyrobetaine hydroxylase.
Rydzik et al. (2014)
1 more