6R9Z

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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular determinants of the mechanism and substrate specificity ofClostridium difficileproline-proline endopeptidase-1.

Pichlo, C.Juetten, L.Wojtalla, F.Schacherl, M.Diaz, D.Baumann, U.

(2019) J Biol Chem 294: 11525-11535

  • DOI: https://doi.org/10.1074/jbc.RA119.009029
  • Primary Citation of Related Structures:  
    6R4W, 6R4X, 6R4Y, 6R4Z, 6R50, 6R51, 6R52, 6R53, 6R54, 6R55, 6R56, 6R57, 6R58, 6R59, 6R5A, 6R5B, 6R5C, 6R9Z

  • PubMed Abstract: 

    Pro-Pro endopeptidase-1 (PPEP-1) is a secreted metalloprotease from the bacterial pathogen Clostridium difficile 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 2+ 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 C. difficile .


  • Organizational Affiliation

    Department of Chemistry, Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACE-GLU-VAL-ASN-PRO-PRO-VAL-PRO-NH29Clostridioides difficileMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2019-06-19 
  • Deposition Author(s): Diaz, D.

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references