3E7A

Crystal Structure of Protein Phosphatase-1 Bound to the natural toxin Nodularin-R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structures of protein phosphatase-1 bound to nodularin-R and tautomycin: a novel scaffold for structure-based drug design of serine/threonine phosphatase inhibitors

Kelker, M.S.Page, R.Peti, W.

(2009) J.Mol.Biol. 385: 11-21

  • DOI: 10.1016/j.jmb.2008.10.053
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein phosphatase 1 occurs in all tissues and regulates many pathways, ranging from cell-cycle progression to carbohydrate metabolism. Many naturally occurring, molecular toxins modulate PP1 activity, though the exact mechanism of this differential ...

    Protein phosphatase 1 occurs in all tissues and regulates many pathways, ranging from cell-cycle progression to carbohydrate metabolism. Many naturally occurring, molecular toxins modulate PP1 activity, though the exact mechanism of this differential regulation is not understood. A detailed elucidation of these interactions is crucial for understanding the cellular basis of phosphatase function and signaling pathways but, more importantly, they can serve as the basis for highly specific therapeutics, e.g. against cancer. We report the crystal structures of PP1 in complex with nodularin-R at 1.63 A and tautomycin at 1.70 A resolution. The PP1:nodularin-R complex was used to demonstrate the utility of our improved PP1 production technique, which produces highly active, soluble PP1. Tautomycin is one of the few toxins that reportedly preferentially binds PP1>PP2A. Therefore, the PP1:tautomycin structure is the first complex structure with a toxin with preferred PP1 specificity. Furthermore, since tautomycin is a linear non-peptide-based toxin, our reported structure will aid the design of lead compounds for novel PP1-specific pharmaceuticals.


    Organizational Affiliation

    Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02903, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
A, B
299Homo sapiensMutation(s): 0 
Gene Names: PPP1CA (PPP1A)
EC: 3.1.3.16
Find proteins for P62136 (Homo sapiens)
Go to Gene View: PPP1CA
Go to UniProtKB:  P62136
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
nodularin R
C, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

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Download CCD File 
B
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000214
Query on PRD_000214
C,DNODULARIN-ROligopeptide / Toxin

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X9AIC50: 0.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.354α = 90.00
b = 77.274β = 90.00
c = 132.444γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2013-02-27
    Type: Other
  • Version 1.3: 2013-04-10
    Type: Derived calculations
  • Version 1.4: 2017-10-25
    Type: Advisory, Refinement description