1H2Y

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

  • DOI: 10.1074/jbc.M208043200
  • Primary Citation of Related Structures:  
    1H2Z, 1H2Y, 1H2X, 1H2W

  • PubMed Abstract: 
  • Prolyl oligopeptidase, a member of a new family of serine peptidases, plays an important role in memory disorders. Earlier x-ray crystallographic investigations indicated that stabilization of the tetrahedral transition state of the reaction involved ...

    Prolyl oligopeptidase, a member of a new family of serine peptidases, plays an important role in memory disorders. Earlier x-ray crystallographic investigations indicated that stabilization of the tetrahedral transition state of the reaction involved hydrogen bond formation between the oxyanion of the tetrahedral intermediate and the OH group of Tyr(473). The contribution of the OH group was tested with the Y473F variant using various substrates. The charged succinyl-Gly-Pro-4-nitroanilide was hydrolyzed with a much lower k(cat)/K(m) compared with the neutral benzyloxycarbonyl-G1y-Pro-2-naphthylamide, although the binding modes of the two substrates were similar, as shown by x-ray crystallography. This suggested that electrostatic interactions between Arg(643) and the succinyl group competed with the productive binding mechanism. Unlike most enzyme reactions, catalysis by the wild-type enzyme exhibited positive activation entropy. In contrast, the activation entropy for the Y473F variant was negative, suggesting that the tyrosine OH group is involved in stabilizing both the transition state and the water shell at the active site. Importantly, Tyr(473) is also implicated in the formation of the enzyme-substrate complex. The nonlinear Arrhenius plot suggested a greater significance of the oxyanion binding site at physiological temperature. The results indicated that Tyr(473) was more needed at high pH, at high temperature, and with charged substrates exhibiting "internally competitive inhibition."


    Related Citations: 
    • 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, H-1518 Budapest, 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
Find proteins for P23687 (Sus scrofa)
Explore P23687 
Go to UniProtKB:  P23687
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZPR
Query on ZPR

Download CCD File 
A
N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL
C18 H22 N2 O4
ORZXYSPOAVJYRU-HOTGVXAUSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZPRKi:  0.3499999940395355   nM  BindingDB
ZPRKi:  4.300000190734863   nM  BindingDB
ZPRIC50:  0.33000001311302185   nM  BindingDB
ZPRIC50:  1.100000023841858   nM  BindingDB
ZPRKi:  0.3499999940395355   nM  BindingDB
ZPRKi:  0.20999999344348907   nM  BindingDB
ZPRIC50:  54   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000692 (ZPR)
Query on PRD_000692
AZ-PRO-PROLINALPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.8α = 90
b = 99.6β = 90
c = 110.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2002-08-20 
  • Released Date: 2002-11-11 
  • Deposition Author(s): Rea, D., Fulop, V.

Revision History 

  • Version 1.0: 2002-11-11
    Type: Initial release
  • Version 1.1: 2011-09-14
    Changes: Derived calculations, Non-polymer description, Source and taxonomy, Version format compliance
  • Version 1.2: 2013-03-06
    Changes: Other