1E8N

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED WITH PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • DOI: 10.1074/jbc.M007003200
  • Primary Citation of Related Structures:  1E8M
  • Also Cited By: 1H2W, 1H2Y, 1H2Z, 1O6F, 1O6G, 1UOO, 1UOP, 1UOQ, 1VZ2, 1VZ3, 1H2X

  • PubMed Abstract: 
  • Structure determination of the inactive S554A variant of prolyl oligopeptidase complexed with an octapeptide has shown that substrate binding is restricted to the P4-P2' region. In addition, it has revealed a hydrogen bond network of potential cataly ...

    Structure determination of the inactive S554A variant of prolyl oligopeptidase complexed with an octapeptide has shown that substrate binding is restricted to the P4-P2' region. In addition, it has revealed a hydrogen bond network of potential catalytic importance not detected in other serine peptidases. This involves a unique intramolecular hydrogen bond between the P1' amide and P2 carbonyl groups and another between the P2' amide and Nepsilon2 of the catalytic histidine 680 residue. It is argued that both hydrogen bonds promote proton transfer from the imidazolium ion to the leaving group. Another complex formed with the product-like inhibitor benzyloxycarbonyl-glycyl-proline, indicating that the carboxyl group of the inhibitor forms a hydrogen bond with the Nepsilon2 of His(680). Because a protonated histidine makes a stronger interaction with the carboxyl group, it offers a possibility of the determination of the real pK(a) of the catalytic histidine residue. This was found to be 6.25, lower than that of the well studied serine proteases. The new titration method gave a single pK(a) for prolyl oligopeptidase, whose reaction exhibited a complex pH dependence for k(cat)/K(m), and indicated that the observed pK(a) values are apparent. The procedure presented may be applicable for other serine peptidases.


    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


    Organizational Affiliation

    Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.




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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE INHIBITOR
I
9N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BE2
Query on BE2
I
L-PEPTIDE LINKINGC7 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.700α = 90.00
b = 99.700β = 90.00
c = 110.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-09-27 
  • Released Date: 2001-01-16 
  • Deposition Author(s): Fulop, V.

Revision History 

  • Version 1.0: 2001-01-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2016-12-28
    Type: Source and taxonomy