5JWI

Crystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Glu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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This is version 1.1 of the entry. See complete history


Literature

Bacterial protease uses distinct thermodynamic signatures for substrate recognition.

Bezerra, G.A.Ohara-Nemoto, Y.Cornaciu, I.Fedosyuk, S.Hoffmann, G.Round, A.Marquez, J.A.Nemoto, T.K.Djinovic-Carugo, K.

(2017) Sci Rep 7: 2848-2848

  • DOI: https://doi.org/10.1038/s41598-017-03220-y
  • Primary Citation of Related Structures:  
    5JWF, 5JWG, 5JWI, 5JXF, 5JXK, 5JXP, 5JY0

  • PubMed Abstract: 

    Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.


  • Organizational Affiliation

    Department of Structural & Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna Biocenter Campus 5, A-1030, Vienna, Austria. gustavo.bezerra@univie.ac.at.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Asp/Glu-specific dipeptidyl-peptidase
A, B
703Porphyromonas endodontalisMutation(s): 1 
Gene Names: dpp11PeDPP11
EC: 3.4.14
UniProt
Find proteins for F8WQK8 (Porphyromonas endodontalis (strain ATCC 35406 / BCRC 14492 / JCM 8526 / NCTC 13058 / HG 370))
Explore F8WQK8 
Go to UniProtKB:  F8WQK8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8WQK8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.441α = 90
b = 112.534β = 90
c = 148.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references