4ZVZ

Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C.

Chattopadhyay, D.Swingle, M.R.Salter, E.A.Wood, E.D'Arcy, B.Zivanov, C.Abney, K.Musiyenko, A.Rusin, S.F.Kettenbach, A.Yet, L.Schroeder, C.E.Golden, J.E.Dunham, W.H.Gingras, A.C.Banerjee, S.Forbes, D.Wierzbicki, A.Honkanen, R.E.

(2016) Biochem. Pharmacol. 109: 14-26

  • DOI: 10.1016/j.bcp.2016.03.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism a ...

    Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure-activity relationship studies and analysis of high-resolution (1.25Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases.


    Related Citations: 
    • Structural basis for the catalytic activity of human serine/threonine protein phosphatase-5.
      Swingle, M.R.,Honkanen, R.E.,Ciszak, E.M.
      (2004) J.Biol.Chem. 279: 33992


    Organizational Affiliation

    Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA; Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA.,Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.,Northeastern Collaborative Access Team (NE-CAT) Cornell University, Lemont, IL, USA.,Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.,Department of Medicine, University of Alabama Birmingham, Birmingham, AL 35294, USA.,Department of Medicinal Chemistry, University of Kansas Specialized Chemistry Center, Lawrence, KS 66047, USA.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA. Electronic address: rhonkanen@southalabama.edu.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 5
A, B, C, D
333Homo sapiensMutation(s): 0 
Gene Names: PPP5C (PPP5)
EC: 3.1.3.16
Find proteins for P53041 (Homo sapiens)
Go to Gene View: PPP5C
Go to UniProtKB:  P53041
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
4TF
Query on 4TF

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Download CCD File 
A, B, C, D
(1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
C12 H18 O6
KENGHAXMPKBHLS-CHHOWFRJSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.858α = 88.15
b = 80.520β = 87.33
c = 91.165γ = 86.71
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2017-02-08
    Type: Database references