› 6evl

X-ray diffraction
1.87Å resolution

Crystal structure of an unlignaded peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase

Released:
DOI: 10.2210/pdb6evl/pdb
PDB entry 6evl coloured by chain, front view.
PDB entry 6evl coloured by chain, side view.
PDB entry 6evl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural enzymology binding studies of the peptide-substrate-binding domain of human collagen prolyl 4-hydroxylase (type-II): High affinity peptides have a PxGP sequence motif.
Murthy AV, Sulu R, Koski MK, Tu H, Anantharajan J, Sah-Teli SK, Myllyharju J, Wierenga RK
Protein Sci 27 1692-1703 (2018)
PMID: 30168208

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127484 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prolyl 4-hydroxylase subunit alpha-2 Chain: A
Molecule details ›
Chain: A
Length: 102 amino acids
Theoretical weight: 11.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O15460 (Residues: 163-257; Coverage: 19%)
Gene names: P4HA2, UNQ290/PRO330
Structure domains: Tetratricopeptide repeat domain

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand DMS 1 x DMS
Ligand GLY 2 x GLY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR
Spacegroup: P3221
Unit cell:
a: 55.449Å b: 55.449Å c: 71.705Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.182 0.224
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Role of prolyl hydroxylation in the molecular interactions of collagens.
Rappu et al. (2019)
3 other articles

2 mentions without citation

Structural enzymology binding studies of the peptide-substrate-binding domain of human collagen prolyl 4-hydroxylase (type-II): High affinity peptides have a PxGP sequence motif.
Murthy et al. (2018)
1 more