5OLJ

Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 and structure-activity relationships based on inhibitor profiling.

Rea, D.Van Elzen, R.De Winter, H.Van Goethem, S.Landuyt, B.Luyten, W.Schoofs, L.Van Der Veken, P.Augustyns, K.De Meester, I.Fulop, V.Lambeir, A.M.

(2017) Eur J Med Chem 139: 482-491

  • DOI: 10.1016/j.ejmech.2017.08.024

  • PubMed Abstract: 
  • The Gram-negative anaerobe Porphyromonas gingivalis is associated with chronic periodontitis. Clinical isolates of P. gingivalis strains with high dipeptidyl peptidase 4 (DPP4) expression also had a high capacity for biofilm formation and were more i ...

    The Gram-negative anaerobe Porphyromonas gingivalis is associated with chronic periodontitis. Clinical isolates of P. gingivalis strains with high dipeptidyl peptidase 4 (DPP4) expression also had a high capacity for biofilm formation and were more infective. The X-ray crystal structure of P. gingivalis DPP4 was solved at 2.2 Å resolution. Despite a sequence identity of 32%, the overall structure of the dimer was conserved between P. gingivalis DPP4 and mammalian orthologues. The structures of the substrate binding sites were also conserved, except for the region called S2-extensive, which is exploited by specific human DPP4 inhibitors currently used as antidiabetic drugs. Screening of a collection of 450 compounds as inhibitors revealed a structure-activity relationship that mimics in part that of mammalian DPP9. The functional similarity between human and bacterial DPP4 was confirmed using 124 potential peptide substrates.


    Related Citations: 
    • Expression, purification and preliminary crystallographic analysis of dipeptidyl peptidase IV from Porphyromonas gingivalis.
      Rea, D.,Lambeir, A.M.,Kumagai, Y.,De Meester, I.,Scharpe, S.,Fulop, V.
      (2004) Acta Crystallogr. D Biol. Crystallogr. 60: 1871


    Organizational Affiliation

    School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase IV
A
723Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)Mutation(s): 0 
Gene Names: dppIV
Find proteins for B2RKU3 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Go to UniProtKB:  B2RKU3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.100α = 90.00
b = 109.100β = 90.00
c = 157.810γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-27 
  • Released Date: 2017-09-06 
  • Deposition Author(s): Fulop, V.

Funding OrganizationLocationGrant Number
Fund for Scientific Research (FWO-Flanders)BelgiumG.0173.09N
Agency for Innovation by Science and Technology in Flanders (IWT, Belgium)BelgiumSBO 50164
Industrial Research Fund of the University of LeuvenBelgiumIOF/KP/09/003
European UnionBelgium223077 (NEUROPRO)

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release