1VZ2

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y73C/V427C/C255T MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Concerted Structural Changes in the Peptidase and the Propeller Domains of Prolyl Oligopeptidase are Required for Substrate Binding

Szeltner, Z.Rea, D.Juhasz, T.Renner, V.Fulop, V.Polgar, L.

(2004) J.Mol.Biol. 340: 627

  • DOI: 10.1016/j.jmb.2004.05.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Prolyl oligopeptidase contains a peptidase domain and its catalytic triad is covered by the central tunnel of a seven-bladed beta-propeller. This domain makes the enzyme an oligopeptidase by excluding large structured peptides from the active site. T ...

    Prolyl oligopeptidase contains a peptidase domain and its catalytic triad is covered by the central tunnel of a seven-bladed beta-propeller. This domain makes the enzyme an oligopeptidase by excluding large structured peptides from the active site. The apparently rigid crystal structure does not explain how the substrate can approach the catalytic groups. Two possibilities of substrate access were investigated: either blades 1 and 7 of the propeller domain move apart, or the peptidase and/or propeller domains move to create an entry site at the domain interface. Engineering disulfide bridges to the expected oscillating structures prevented such movements, which destroyed the catalytic activity and precluded substrate binding. This indicated that concerted movements of the propeller and the peptidase domains are essential for the enzyme action.


    Related Citations: 
    • Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism
      Fulop, V.,Szeltner, Z.,Polgar, L.
      (2000) Embo Rep. 1: 277
    • Electrostatic Environment at the Active Site of Prolyl Oligopeptidase is Highly Influential During Substrate Binding
      Szeltner, Z.,Rea, D.,Renner, V.,Juliano, L.,Fulop, V.,Polgar, L.
      (2003) J.Biol.Chem. 278: 48786
    • Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Binding for Titration of the Catalytic Histidine Residue
      Fulop, V.,Szeltner, Z.,Renner, V.,Polgar, L.
      (2001) J.Biol.Chem. 276: 1262
    • Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis
      Fulop, V.,Bocskei, Z.,Polgar, L.
      (1998) Cell 94: 161
    • Electrostatic Effects and Binding Determinants in the Catalysis of Prolyl Oligopeptidase: Site Specific Mutagenesis at the Oxyanion Binding Site
      Szeltner, Z.,Rea, D.,Renner, V.,Fulop, V.,Polgar, L.
      (2002) J.Biol.Chem. 277: 42613
    • Substrate-Dependent Competency of the Catalytic Triad of Prolyl Oligopeptidase
      Szeltner, Z.,Rea, D.,Juhasz, T.,Renner, V.,Mucsi, Z.,Orosz, G.,Fulop, V.,Polgar, L.
      (2002) J.Biol.Chem. 277: 44597


    Organizational Affiliation

    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest 112, P.O. Box 7, Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROLYL ENDOPEPTIDASE
A
710Sus scrofaMutation(s): 3 
Gene Names: PREP
EC: 3.4.21.26
Find proteins for P23687 (Sus scrofa)
Go to Gene View: PREP
Go to UniProtKB:  P23687
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: 0.208 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.900α = 90.00
b = 99.600β = 90.00
c = 110.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4phasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2004-05-14 
  • Released Date: 2004-07-01 
  • Deposition Author(s): Rea, D., Fulop, V.

Revision History 

  • Version 1.0: 2004-07-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance