1O6F

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641A MUTANT WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • DOI: 10.1074/jbc.M207386200
  • Primary Citation of Related Structures:  1O6G
  • Also Cited By: 1UOO, 1UOP, 1UOQ, 1VZ2, 1VZ3

  • PubMed Abstract: 
  • Prolyl oligopeptidase, a serine peptidase unrelated to trypsin and subtilisin, is implicated in memory disorders and is an important target of drug design. The catalytic competence of the Asp(641) residue of the catalytic triad (Ser(554), Asp(641), H ...

    Prolyl oligopeptidase, a serine peptidase unrelated to trypsin and subtilisin, is implicated in memory disorders and is an important target of drug design. The catalytic competence of the Asp(641) residue of the catalytic triad (Ser(554), Asp(641), His(680)) was studied using the D641N and D641A variants of the enzyme. Both variants displayed 3 orders of magnitude reduction in k(cat)/K(m) for benzyloxycarbonyl-Gly-Pro-2-naphthylamide. Using an octapeptide substrate, the decrease was 6 orders of magnitude, whereas with Z-Gly-Pro-4-nitrophenyl ester there was virtually no change in k(cat)/K(m). This indicates that the contribution of Asp(641) is very much dependent on the substrate-leaving group, which was not the case for the classic serine peptidase, trypsin. The rate constant for benzyloxycarbonyl-Gly-Pro-thiobenzylester conformed to this series as demonstrated by a method designed for monitoring the hydrolysis of thiolesters in the presence of thiol groups. Alkylation of His(680) with Z-Gly-Pro-CH(2)Cl was concluded with similar rate constants for wild-type and D641A variant. However, kinetic measurements with Z-Gly-Pro-OH, a product-like inhibitor, indicated that the His(680) is not accessible in the enzyme variants. Crystal structure determination of these mutants revealed subtle perturbations related to the catalytic activity. Many of these observations show differences in the catalysis between trypsin and prolyl oligopeptidase.


    Related Citations: 
    • Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis
      Fulop, V.,Bocskei, Z.,Polgar, L.
      (1998) Cell 94: 161
    • Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism
      Fulop, V.,Szeltner, Z.,Polgar, L.
      (2000) Embo Rep. 1: 277
    • Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Bindtitration of the Catalytic Histidine Residueing for
      Fulop, V.,Szeltner, Z.,Renner, V.,Polgar, L.
      (2001) J.Biol.Chem. 276: 1262


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROLYL ENDOPEPTIDASE
A
710Sus scrofaGene 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
SIN
Query on SIN

Download SDF File 
Download CCD File 
A
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
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
PRO
Query on PRO

Download SDF File 
Download CCD File 
A
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.400α = 90.00
b = 100.200β = 90.00
c = 111.300γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
X-PLORphasing
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-09-15 
  • Released Date: 2002-11-18 
  • Deposition Author(s): Rea, D., Fulop, V.

Revision History 

  • Version 1.0: 2002-11-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance