5E3A

Structure of human DPP3 in complex with opioid peptide leu-enkephalin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition.

Kumar, P.Reithofer, V.Reisinger, M.Wallner, S.Pavkov-Keller, T.Macheroux, P.Gruber, K.

(2016) Sci Rep 6: 23787-23787

  • DOI: 10.1038/srep23787
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also im ...

    Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also implicated in several forms of cancer. We present high-resolution crystal structures of hDPP III in complex with opioid peptides (Met-and Leu-enkephalin, endomorphin-2) as well as with angiotensin-II and the peptide inhibitor IVYPW. These structures confirm the previously reported large conformational change of the enzyme upon ligand binding and show that the structure of the closed conformation is independent of the nature of the bound peptide. The overall peptide-binding mode is also conserved ensuring the correct positioning of the scissile peptide bond with respect to the catalytic zinc ion. The structure of the angiotensin-II complex shows, how longer peptides are accommodated in the binding cleft of hDPP III. Differences in the binding modes allow a distinction between real substrates and inhibitory peptides or "slow" substrates. The latter displace a zinc bound water molecule necessitating the energetically much less favoured anhydride mechanism as opposed to the favoured promoted-water mechanism. The structural data also form the necessary framework for the design of specific hDPP III inhibitors.


    Organizational Affiliation

    ACIB - Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.,BioTechMed-Graz, Austria.,Institute of Molecular Biosciences, University of Graz, Humboldtstra├če 50/3, 8010 Graz, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 3
A
726Homo sapiensMutation(s): 6 
Gene Names: DPP3
EC: 3.4.14.4
Find proteins for Q9NY33 (Homo sapiens)
Go to Gene View: DPP3
Go to UniProtKB:  Q9NY33
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Leu-enkephalin
B
5Homo sapiensMutation(s): 0 
Gene Names: PENK
Find proteins for P01210 (Homo sapiens)
Go to Gene View: PENK
Go to UniProtKB:  P01210
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.558α = 90.00
b = 105.757β = 93.43
c = 64.992γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaW901

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 2.0: 2017-09-06
    Type: Atomic model, Author supporting evidence