› 5yzo

X-ray diffraction
1.7Å resolution

Crystal structure of S9 peptidase mutant (S514A) from Deinococcus radiodurans R1

Released:
DOI: 10.2210/pdb5yzo/pdb
PDB entry 5yzo coloured by chain, front view.
PDB entry 5yzo coloured by chain, side view.
PDB entry 5yzo coloured by chain, top view.
Source organism: Deinococcus radiodurans R1
Primary publication:
Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms.
Yadav P, Goyal VD, Gaur NK, Kumar A, Gokhale SM, Jamdar SN, Makde RD
J Biol Chem 294 89-100 (2019)
PMID: 30409909

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193343 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase S9 prolyl oligopeptidase catalytic domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 656 amino acids
Theoretical weight: 72.71 KDa
Source organism: Deinococcus radiodurans R1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9RXY9 (Residues: 2-655; Coverage: 100%)
Gene name: DR_0165
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand DMS 9 x DMS
Ligand GOL 6 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Spacegroup: P21
Unit cell:
a: 77.195Å b: 190.015Å c: 119.548Å
α: 90° β: 108.46° γ: 90°
R-values:
R R work R free
0.17 0.168 0.194
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 citation in other articles

The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements.
Denesyuk et al. (2020)
5 more

2 mentions without citation

Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms.
Yadav et al. (2019)
1 more