› 6evp

X-ray diffraction
1.68Å resolution

Crystal structure the peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Glu-Gly-Pro-Pro-Gly.

Released:
DOI: 10.2210/pdb6evp/pdb
PDB entry 6evp coloured by chain, front view.
PDB entry 6evp coloured by chain, side view.
PDB entry 6evp coloured by chain, top view.
Source organisms:
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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127489 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
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
PRO-PRO-GLY-PRO-GLU-GLY-PRO-PRO-GLY Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 804 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P3221
Unit cell:
a: 55.02Å b: 55.02Å c: 73.269Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.183 0.215
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

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

4 mentions without citation

Solution Structure of the Carboxy-Terminal Tandem Repeat Domain of Eukaryotic Elongation Factor 2 Kinase and Its Role in Substrate Recognition.
Piserchio et al. (2019)
3 more