1UOO

Prolyl oligopeptidase from porcine brain, S554A mutant with bound peptide ligand GLY-PHE-ARG-PRO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

  • DOI: 10.1074/jbc.M309555200
  • Primary Citation of Related Structures:  
    1UOQ, 1UOP, 1UOO

  • PubMed Abstract: 
  • The positive electrostatic environment of the active site of prolyl oligopeptidase was investigated by using substrates with glutamic acid at positions P2, P3, P4, and P5, respectively. The different substrates gave various pH rate profiles. The pKa values extracted from the curves are apparent parameters, presumably affected by the nearby charged residues, and do not reflect the ionization of a simple catalytic histidine as found in the classic serine peptidases like chymotrypsin and subtilisin ...

    The positive electrostatic environment of the active site of prolyl oligopeptidase was investigated by using substrates with glutamic acid at positions P2, P3, P4, and P5, respectively. The different substrates gave various pH rate profiles. The pKa values extracted from the curves are apparent parameters, presumably affected by the nearby charged residues, and do not reflect the ionization of a simple catalytic histidine as found in the classic serine peptidases like chymotrypsin and subtilisin. The temperature dependence of kcat/Km did not produce linear Arrhenius plots, indicating different changes in the individual rate constants with the increase in temperature. This rendered it possible to calculate these constants, i.e. the formation (k1) and decomposition (k-1) of the enzyme-substrate complex and the acylation constant (k2), as well as the corresponding activation energies. The results have revealed the relationship between the complex Michaelis parameters and the individual rate constants. Structure determination of the enzyme-substrate complexes has shown that the different substrates display a uniform binding mode. None of the glutamic acids interacts with a charged group. We conclude that the specific rate constant is controlled by k1 rather than k2 and that the charged residues from the substrate and the enzyme can markedly affect the formation but not the structure of the enzyme-substrate complexes.


    Related Citations: 
    • 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
    • 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
    • Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism
      Fulop, V., Szeltner, Z., Polgar, L.
      (2000) EMBO Rep 1: 277
    • Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis
      Fulop, V., Bocskei, Z., Polgar, L.
      (1998) Cell 94: 161

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROLYL ENDOPEPTIDASEA710Sus scrofaMutation(s): 1 
Gene Names: PREP
EC: 3.4.21.26
UniProt
Find proteins for P23687 (Sus scrofa)
Explore P23687 
Go to UniProtKB:  P23687
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE LIGAND GLY-PHE-ARG-PROB4synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.2α = 90
b = 98.7β = 90
c = 109.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2003-09-22 
  • Released Date: 2003-10-02 
  • Deposition Author(s): Rea, D., Fulop, V.

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-02
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Data collection, Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection