› 4lit

X-ray diffraction
2.4Å resolution

Structure of YcfD a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and 2-oxoglutarate.

Released:
DOI: 10.2210/pdb4lit/pdb
PDB entry 4lit coloured by chain, front view.
PDB entry 4lit coloured by chain, side view.
PDB entry 4lit coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JRC, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ
Nature 510 422-426 (2014)
PMID: 24814345

Function and Biology Details

Reaction catalysed: 
[50S ribosomal protein L16]-L-Arg(81) + 2-oxoglutarate + O(2) = [50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg(81) + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151001 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal protein uL16 3-hydroxylase Chain: A
Molecule details ›
Chain: A
Length: 407 amino acids
Theoretical weight: 46.18 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P27431 (Residues: 1-373; Coverage: 100%)
Gene names: JW1114, b1128, roxA, ycfD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand CO 1 x CO
Ligand AKG 1 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P43212
Unit cell:
a: 74.14Å b: 74.14Å c: 208.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.236
Expression system: Escherichia coli

Quick links

Citations

22 review citations

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

2 mentions without citation

JMJD5 is a human arginyl C-3 hydroxylase.
Wilkins et al. (2018)
1 more