› 6ax6

X-ray diffraction
2.24Å resolution

The crystal structure of a lysyl hydroxylase from Acanthamoeba polyphaga mimivirus

Released:
DOI: 10.2210/pdb6ax6/pdb
PDB entry 6ax6 coloured by chain, front view.
PDB entry 6ax6 coloured by chain, side view.
PDB entry 6ax6 coloured by chain, top view.
Source organism: Acanthamoeba polyphaga mimivirus
Primary publication:
Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding.
Guo HF, Tsai CL, Terajima M, Tan X, Banerjee P, Miller MD, Liu X, Yu J, Byemerwa J, Alvarado S, Kaoud TS, Dalby KN, Bota-Rabassedas N, Chen Y, Yamauchi M, Tainer JA, Phillips GN, Kurie JM
Nat Commun 9 512 (2018)
PMID: 29410444

Function and Biology Details

Reaction catalysed: 
L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO(2)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178385 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Procollagen lysyl hydroxylase and glycosyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 235 amino acids
Theoretical weight: 27.35 KDa
Source organism: Acanthamoeba polyphaga mimivirus
Expression system: Not provided
UniProt:
  • Canonical: Q5UQC3 (Residues: 680-895; Coverage: 24%)
Gene name: MIMI_L230

Ligands and Environments

2 bound ligands:
Ligand IOD 68 x IOD
Ligand FE2 2 x FE2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P43212
Unit cell:
a: 109.21Å b: 109.21Å c: 83.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.223 0.24
Expression system: Not provided

Quick links

Citations

6 review citations

Iron Metabolism in Cancer.
Wang et al. (2018)
5 more

3 mentions without citation

The Astounding World of Glycans from Giant Viruses.
Speciale et al. (2022)
2 more