› 5x49

X-ray diffraction
1.65Å resolution

Crystal Structure of Human mitochondrial X-prolyl Aminopeptidase (XPNPEP3)

Released:
DOI: 10.2210/pdb5x49/pdb
PDB entry 5x49 coloured by chain, front view.
PDB entry 5x49 coloured by chain, side view.
PDB entry 5x49 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes.
Singh R, Jamdar SN, Goyal VD, Kumar A, Ghosh B, Makde RD
J Biol Chem 292 10035-10047 (2017)
PMID: 28476889

Function and Biology Details

Reaction catalysed: 
Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192507 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Xaa-Pro aminopeptidase 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 456 amino acids
Theoretical weight: 51.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NQH7 (Residues: 54-507; Coverage: 90%)
Gene name: XPNPEP3
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand MN 4 x MN
Ligand 12P 2 x 12P
Ligand 01B 2 x 01B
Ligand DMS 6 x DMS
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Spacegroup: P21
Unit cell:
a: 62.897Å b: 135.103Å c: 67.205Å
α: 90° β: 99.87° γ: 90°
R-values:
R R work R free
0.155 0.154 0.178
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Mitochondrial Protein Homeostasis and Cardiomyopathy.
Wachoski-Dark et al. (2022)
3 more

1 mention without citation

Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes.
Singh et al. (2017)