› 5z48

X-ray diffraction
1.55Å resolution

Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate

Released:
DOI: 10.2210/pdb5z48/pdb
PDB entry 5z48 coloured by chain, front view.
PDB entry 5z48 coloured by chain, side view.
PDB entry 5z48 coloured by chain, top view.
Source organism: Deinococcus radiodurans R1
Primary publication:
Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition.
Agrawal R, Singh R, Kumar A, Kumar A, Makde RD
Acta Crystallogr D Struct Biol 75 308-316 (2019)
PMID: 30950401

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193324 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolidone-carboxylate peptidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 220 amino acids
Theoretical weight: 23.26 KDa
Source organism: Deinococcus radiodurans R1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RX25 (Residues: 1-218; Coverage: 100%)
Gene names: DR_0490, pcp
Sequence domains: Pyroglutamyl peptidase
Structure domains: Peptidase C15, pyroglutamyl peptidase I-like

Ligands and Environments

3 bound ligands:
Ligand NA 2 x NA
Ligand DMS 3 x DMS
Ligand PCA 2 x PCA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Unit cell:
a: 89.069Å b: 46.918Å c: 105.584Å
α: 90° β: 105.51° γ: 90°
R-values:
R R work R free
0.16 0.158 0.186
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Pyroglutamyl aminopeptidase 1 is a potential molecular target toward diagnosing and treating inflammation.
Jiang et al. (2023)