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 

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Ligand Structure Quality Assessment 


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, 4AN0, 4AN1

  • 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 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROLYL ENDOPEPTIDASEA710Sus scrofaMutation(s): 0 
Gene Names: PREP
EC: 3.4.21.26
UniProt
Find proteins for P23687 (Sus scrofa)
Explore P23687 
Go to UniProtKB:  P23687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23687
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2P6
Query on 2P6

Download Ideal Coordinates CCD File 
B [auth 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 Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2P6 BindingDB:  4AN0 Ki: min: 0.02, max: 0.95 (nM) from 7 assay(s)
IC50: min: 0.2, max: 6 (nM) from 5 assay(s)
PDBBind:  4AN0 Ki: 0.02 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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