4AN0

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 1398-1411

  • DOI: 10.1016/j.biochi.2012.03.012
  • Primary Citation of Related Structures:  
    4AMY, 4AMZ, 4AN1, 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROLYL ENDOPEPTIDASEA710Sus scrofaMutation(s): 0 
Gene Names: PREP
EC: 3.4.21.26
Find proteins for P23687 (Sus scrofa)
Explore P23687 
Go to UniProtKB:  P23687
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2P6
Query on 2P6

Download CCD File 
A
(2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile
C20 H25 N3 O2
SPXFAUXQZWJGCJ-ROUUACIJSA-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 %)
2P6Ki:  0.019999999552965164   nM  BindingDB
2P6Ki:  0.9200000166893005   nM  BindingDB
2P6Ki:  0.949999988079071   nM  BindingDB
2P6Ki:  0.10000000149011612   nM  BindingDB
2P6Ki :  0.019999999552965164   nM  PDBBind
2P6IC50:  6   nM  BindingDB
2P6Ki:  0.019999999552965164   nM  BindingDB
2P6IC50:  0.20000000298023224   nM  BindingDB
2P6IC50:  0.2199999988079071   nM  BindingDB
2P6Ki:  0.019999999552965164   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.3α = 90
b = 99.9β = 90
c = 111.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Structure summary
  • Version 1.2: 2018-11-14
    Changes: Data collection, Database references