5JWG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


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:  
    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 ...

    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 Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Asp/Glu-specific dipeptidyl-peptidaseA, B703Porphyromonas 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
ASP
Query on ASP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.81α = 90
b = 114.403β = 90
c = 147.824γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
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