› 5z47

X-ray diffraction
1.7Å resolution

Crystal structure of pyrrolidone carboxylate peptidase I with disordered loop A from Deinococcus radiodurans R1

Released:
DOI: 10.2210/pdb5z47/pdb
PDB entry 5z47 coloured by chain, front view.
PDB entry 5z47 coloured by chain, side view.
PDB entry 5z47 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: 23.28 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

1 bound ligand:
Ligand DMS 2 x DMS
1 modified residue:
Ligand CSX 2 x CSX

Experiments and Validation Details

Entry percentile scores
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Unit cell:
a: 89.317Å b: 47.171Å c: 105.537Å
α: 90° β: 105.66° γ: 90°
R-values:
R R work R free
0.208 0.207 0.239
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)