5JY0

Crystal structure of Porphyromonas endodontalis DPP11 in complex with substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.599 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


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: 10.1038/s41598-017-03220-y
  • Primary Citation of Related Structures:  

  • 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 a ...

    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.,European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, 38042, Grenoble, France.,Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8588, Japan.,European XFEL GmbH, Notkestraße 85, 22607, Hamburg, Germany.,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.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia.,Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, A-1030, Vienna, Austria. gustavo.bezerra@univie.ac.at.,Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, A-1030, Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Asp/Glu-specific dipeptidyl-peptidase
A
703Porphyromonas endodontalis (strain ATCC 35406 / BCRC 14492 / JCM 8526 / NCTC 13058 / HG 370)Mutation(s): 1 
Gene Names: dpp11 (PeDPP11)
EC: 3.4.14.-
Find proteins for F8WQK8 (Porphyromonas endodontalis (strain ATCC 35406 / BCRC 14492 / JCM 8526 / NCTC 13058 / HG 370))
Go to UniProtKB:  F8WQK8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEU-ASP-VAL
B
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.599 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.787α = 90.00
b = 113.331β = 106.26
c = 111.226γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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