› 6r50

X-ray diffraction
1.81Å resolution

Crystal structure of holo PPEP-1(E143A/Y178F) in complex with substrate peptide Ac-EVNAPVP-CONH2

Released:
DOI: 10.2210/pdb6r50/pdb
PDB entry 6r50 coloured by chain, front view.
PDB entry 6r50 coloured by chain, side view.
PDB entry 6r50 coloured by chain, top view.
Source organism: Clostridioides difficile
Primary publication:
Molecular determinants of the mechanism and substrate specificity of Clostridium difficile proline-proline endopeptidase-1.
Pichlo C, Juetten L, Wojtalla F, Schacherl M, Diaz D, Baumann U
J Biol Chem 294 11525-11535 (2019)
PMID: 31182482

Function and Biology Details

Reaction catalysed: 
The enzyme catalyzes the hydrolytic cleavage of peptide bonds between two proline residues
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-553427 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pro-Pro endopeptidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 198 amino acids
Theoretical weight: 21.91 KDa
Source organism: Clostridioides difficile
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q183R7 (Residues: 27-220; Coverage: 100%)
Gene names: CD630_28300, ppep-1, zmp1
Sequence domains: Anthrax toxin lethal factor, N- and C-terminal domain
ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 amino acids
Theoretical weight: 750 Da
Source organism: Clostridioides difficile
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
1 modified residue:
Ligand LPD 2 x LPD

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 37.54Å b: 42.927Å c: 123.45Å
α: 90° β: 95.98° γ: 90°
R-values:
R R work R free
0.147 0.145 0.176
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Thermal Reactivity in Metal Organic Materials (MOMs): From Single-Crystal-to-Single-Crystal Reactions and Beyond.
Martí-Rujas J. (2019)
1 more

1 mention without citation

Molecular determinants of the mechanism and substrate specificity of Clostridium difficile proline-proline endopeptidase-1.
Pichlo et al. (2019)