› 5jz8

X-ray diffraction
2.1Å resolution

Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine, and factor X substrate peptide fragment (39mer)

Released:
DOI: 10.2210/pdb5jz8/pdb
PDB entry 5jz8 coloured by chain, front view.
PDB entry 5jz8 coloured by chain, side view.
PDB entry 5jz8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Aspartate/asparagine-β-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern.
Pfeffer I, Brewitz L, Krojer T, Jensen SA, Kochan GT, Kershaw NJ, Hewitson KS, McNeill LA, Kramer H, Münzel M, Hopkinson RJ, Oppermann U, Handford PA, McDonough MA, Schofield CJ
Nat Commun 10 4910 (2019)
PMID: 31659163

Function and Biology Details

Reactions catalysed: 
Peptide L-aspartate + 2-oxoglutarate + O(2) = peptide 3-hydroxy-L-aspartate + succinate + CO(2)
Selective cleavage of Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133217 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Aspartyl/asparaginyl beta-hydroxylase Chain: A
Molecule details ›
Chain: A
Length: 429 amino acids
Theoretical weight: 49.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12797 (Residues: 330-758; Coverage: 57%)
Gene names: ASPH, BAH
Sequence domains:
Structure domains: B-lactam Antibiotic, Isopenicillin N Synthase; Chain
Factor X light chain Chain: B
Molecule details ›
Chain: B
Length: 39 amino acids
Theoretical weight: 4.25 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00742 (Residues: 86-124; Coverage: 9%)
Gene name: F10
Sequence domains: EGF-like domain

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand OGA 1 x OGA
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 50.244Å b: 91.02Å c: 122.666Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.216
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Aspartate β-hydroxylase as a target for cancer therapy.
Kanwal et al. (2020)
3 more

1 mention without citation

Combined proteomic and biochemical analyses redefine the consensus sequence requirement for epidermal growth factor-like domain hydroxylation.
Brewitz et al. (2022)