6R9Z

3D NMR solution structure of ligand peptide (Ac)EVNPPVP of Pro-Pro endopeptidase-1

Summary for 6R9Z

• Entry DOI: 10.2210/pdb6r9z/pdb
• NMR Information: BMRB: 27863,34391
• Descriptor: ACE-GLU-VAL-ASN-PRO-PRO-VAL-PRO-NH2 (1 entity in total)
• Functional Keywords: synthetic model peptide, pro-pro endopeptidase-1, hydrolase
• Biological source: Clostridioides difficile
• Total number of polymer chains: 1
• Total formula weight: 774.88

Authors

Diaz, D. (deposition date: 2019-04-04, release date: 2019-06-19, Last modification date: 2024-10-16)

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

SOLUTION NMR