6R58

Crystal structure of PPEP-1(E143A/Y178F/E184A) in complex with substrate peptide Ac-EVNAPVP-CONH2

Summary for 6R58

• Entry DOI: 10.2210/pdb6r58/pdb
• Descriptor: Pro-Pro endopeptidase, ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD, ZINC ION, ... (6 entities in total)
• Functional Keywords: pro-pro endopeptidase 1, zinc metallopeptidase, clostridium difficile, virulence factor, hydrolase
• Biological source: Peptoclostridium difficile; More
• Total number of polymer chains: 8
• Total formula weight: 90755.76

Authors

Pichlo, C.,Baumann, U. (deposition date: 2019-03-24, release date: 2019-06-12, Last modification date: 2024-01-24)

Primary citation

Pichlo, C.,Juetten, L.,Wojtalla, F.,Schacherl, M.,Diaz, D.,Baumann, U.
Molecular determinants of the mechanism and substrate specificity ofClostridium difficileproline-proline endopeptidase-1.
J.Biol.Chem., 294:11525-11535, 2019

PubMed Abstract: Pro-Pro endopeptidase-1 (PPEP-1) is a secreted metalloprotease from the bacterial pathogen that cleaves two endogenous adhesion proteins. PPEP-1 is therefore important for bacterial motility and hence for efficient gut colonization during infection. PPEP-1 exhibits a unique specificity for Pro-Pro peptide bonds within the consensus sequence VNP↓PVP. In this study, we combined information from crystal and NMR structures with mutagenesis and enzyme kinetics to investigate the mechanism and substrate specificity of PPEP-1. Our analyses revealed that the substrate-binding cleft of PPEP-1 is shaped complementarily to the major conformation of the substrate in solution. We found that it possesses features that accept a tertiary amide and help discriminate P1' residues by their amide hydrogen bond-donating potential. We also noted that residues Lys-101, Trp-103, and Glu-184 are crucial for proteolytic activity. Upon substrate binding, these residues position a flexible loop over the substrate-binding cleft and modulate the second coordination sphere of the catalytic zinc ion. On the basis of these findings, we propose an induced-fit model in which prestructured substrates are recognized followed by substrate positioning within the active-site cleft and a concomitant increase in the Lewis acidity of the catalytic Zn ion. In conclusion, our findings provide detailed structural and mechanistic insights into the substrate recognition and specificity of PPEP-1 from the common gut pathogen .

PubMed: 31182482
DOI: 10.1074/jbc.RA119.009029

Experimental method

X-RAY DIFFRACTION (1.9 Å)