4AN1

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Dynamics, Crystallography and Mutagenesis Studies on the Substrate Gating Mechanism of Prolyl Oligopeptidase.

Kaszuba, K.Rog, T.Danne, R.Canning, P.Fulop, V.Juhasz, T.Szeltner, Z.St-Pierre, J.F.Garcia-Horsman, A.Mannisto, P.T.Karttunen, M.Hokkanen, J.Bunker, A.

(2012) Biochimie 94: 1398

  • DOI: 10.1016/j.biochi.2012.03.012
  • Primary Citation of Related Structures:  4AMY, 4AMZ, 4AN0

  • PubMed Abstract: 
  • Altered prolyl oligopeptidase (PREP) activity is found in many common neurological and other genetic disorders, and in some cases PREP inhibition may be a promising treatment. The active site of PREP resides in an internal cavity; in addition to the ...

    Altered prolyl oligopeptidase (PREP) activity is found in many common neurological and other genetic disorders, and in some cases PREP inhibition may be a promising treatment. The active site of PREP resides in an internal cavity; in addition to the direct interaction between active site and substrate or inhibitor, the pathway to reach the active site (the gating mechanism) must be understood for more rational inhibitor design and understanding PREP function. The gating mechanism of PREP has been investigated through molecular dynamics (MD) simulation combined with crystallographic and mutagenesis studies. The MD results indicate the inter-domain loop structure, comprised of 3 loops at residues, 189-209 (loop A), 577-608 (loop B), and 636-646 (loop C) (porcine PREP numbering), are important components of the gating mechanism. The results from enzyme kinetics of PREP variants also support this hypothesis: When loop A is (1) locked to loop B through a disulphide bridge, all enzyme activity is halted, (2) nicked, enzyme activity is increased, and (3) removed, enzyme activity is only reduced. Limited proteolysis study also supports the hypothesis of a loop A driven gating mechanism. The MD results show a stable network of H-bonds that hold the two protein domains together. Crystallographic study indicates that a set of known PREP inhibitors inhabit a common binding conformation, and this H-bond network is not significantly altered. Thus the domain separation, seen to occur in lower taxa, is not involved in the gating mechanism for mammalian PREP. In two of the MD simulations we observed a conformational change that involved the breaking of the H-bond network holding loops A and B together. We also found that this network was more stable when the active site was occupied, thus decreasing the likelihood of this transition.


    Organizational Affiliation

    Department of Physics, Tampere University of Technology, Tampere, Finland.




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 2 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
2P8
Query on 2P8

Download SDF File 
Download CCD File 
A
(2S)-N-benzyl-2-({(2S)-2-[(1R)-1,2-dihydroxyethyl]pyrrolidin-1-yl}carbonyl)pyrrolidine-1-carboxamide
C19 H27 N3 O4
KPSYULVHJGJVEA-ULQDDVLXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2P8Ki: 0.055 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.500α = 90.00
b = 99.000β = 90.00
c = 109.400γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Structure summary