› 4s2t

X-ray diffraction
2.15Å resolution

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site

Released:
DOI: 10.2210/pdb4s2t/pdb
PDB entry 4s2t coloured by chain, front view.
PDB entry 4s2t coloured by chain, side view.
PDB entry 4s2t coloured by chain, top view.
Source organism: Caenorhabditis elegans
Primary publication:
Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site.
Iyer S, La-Borde PJ, Payne KA, Parsons MR, Turner AJ, Isaac RE, Acharya KR
FEBS Open Bio 5 292-302 (2015)
PMID: 25905034

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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129197 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Xaa-Pro aminopeptidase app-1 Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 639 amino acids
Theoretical weight: 72.21 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O44750 (Residues: 1-616; Coverage: 100%)
Gene names: W03G9.4, app-1
Sequence domains:
Structure domains:
apstatin Chains: A, B
Molecule details ›
Chains: A, B
Length: 5 amino acids
Theoretical weight: 459 Da
Source organism: Caenorhabditis elegans
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand SO4 7 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: C2
Unit cell:
a: 140.59Å b: 86.81Å c: 113.13Å
α: 90° β: 115.96° γ: 90°
R-values:
R R work R free
0.207 0.205 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 citation in other articles

Intrinsically disordered protein PID-2 modulates Z granules and is required for heritable piRNA-induced silencing in the Caenorhabditis elegans embryo.
Placentino et al. (2021)
5 more

2 mentions without citation

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site.
Iyer et al. (2015)
1 more