3T6B

Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III

Bezerra, G.A.Dobrovetsky, E.Viertlmayr, R.Dong, A.Binter, A.Abramic, M.Macheroux, P.Dhe-Paganon, S.Gruber, K.

(2012) Proc.Natl.Acad.Sci.USA 109: 6525-6530

  • DOI: 10.1073/pnas.1118005109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. He ...

    Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft ("entropy reservoir") as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.


    Organizational Affiliation

    Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 3
A, B
726Homo sapiensMutation(s): 1 
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
Tynorphin
C, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.970α = 90.00
b = 107.550β = 90.67
c = 119.100γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
DNAdata collection
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2013-03-13
    Type: Other
  • Version 1.4: 2013-06-19
    Type: Database references