› 6tp5

X-ray diffraction
2.25Å resolution

Crystal structure of human Transmembrane prolyl 4-hydroxylase

Released:
DOI: 10.2210/pdb6tp5/pdb
PDB entry 6tp5 coloured by chain, front view.
PDB entry 6tp5 coloured by chain, side view.
PDB entry 6tp5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains.
Myllykoski M, Sutinen A, Koski MK, Kallio JP, Raasakka A, Myllyharju J, Wierenga RK, Koivunen P
J Biol Chem 296 100197
PMID: 33334883

Function and Biology Details

Reaction catalysed: 
Hypoxia-inducible factor-L-proline + 2-oxoglutarate + O(2) = hypoxia-inducible factor-trans-4-hydroxy-L-proline + 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-192682 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Transmembrane prolyl 4-hydroxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 421 amino acids
Theoretical weight: 48.35 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NXG6 (Residues: 88-502; Coverage: 83%)
Gene names: P4HTM, PH4
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
6 bound ligands:
Ligand OGA 2 x OGA
Ligand FE2 2 x FE2
Ligand TBU 8 x TBU
Ligand GLY 2 x GLY
Ligand CA 4 x CA
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P31
Unit cell:
a: 92.079Å b: 92.079Å c: 129.5Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.182 0.221
Expression system: Spodoptera frugiperda

Quick links

Citations

3 review citations

HIDEA syndrome is caused by biallelic, pathogenic, rare or founder P4HTM variants impacting the active site or the overall stability of the P4H-TM protein.
Kraatari-Tiri et al. (2022)
2 more

1 mention without citation

Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains.
Myllykoski et al. (2021)