› 2yq8

X-ray diffraction
2.99Å resolution

Crystal structure of the SeMet-labeled N-terminal domain and peptide substrate binding domain of alpha subunit of prolyl-4 hydroxylase type I from human.

Released:
DOI: 10.2210/pdb2yq8/pdb
PDB entry 2yq8 coloured by chain, front view.
PDB entry 2yq8 coloured by chain, side view.
PDB entry 2yq8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase.
Anantharajan J, Koski MK, Kursula P, Hieta R, Bergmann U, Myllyharju J, Wierenga RK
Structure 21 2107-18 (2013)
PMID: 24207127

Function and Biology Details

Reaction catalysed: 
L-proline-[procollagen] + 2-oxoglutarate + O(2) = trans-4-hydroxy-L-proline-[procollagen] + succinate + CO(2)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146694 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prolyl 4-hydroxylase subunit alpha-1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 239 amino acids
Theoretical weight: 27.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13674 (Residues: 18-255; Coverage: 46%)
Gene names: P4HA, P4HA1
Sequence domains: Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
Structure domains:

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: C2
Unit cell:
a: 104.878Å b: 72.017Å c: 66.431Å
α: 90° β: 91.67° γ: 90°
R-values:
R R work R free
0.212 0.209 0.277
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

1 mention without citation

Highly Accessible Computational Prediction and In Vivo/In Vitro Experimental Validation: Novel Synthetic Phenyl Ketone Derivatives as Promising Agents against NAFLD via Modulating Oxidoreductase Activity.
Qiao et al. (2023)