1JK7

CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of the tumor-promoter okadaic acid bound to protein phosphatase-1.

Maynes, J.T.Bateman, K.S.Cherney, M.M.Das, A.K.Luu, H.A.Holmes, C.F.James, M.N.

(2001) J Biol Chem 276: 44078-44082

  • DOI: https://doi.org/10.1074/jbc.M107656200
  • Primary Citation of Related Structures:  
    1JK7

  • PubMed Abstract: 

    Protein phosphatase-1 (PP1) plays a key role in dephosphorylation in numerous biological processes such as glycogen metabolism, cell cycle regulation, smooth muscle contraction, and protein synthesis. Microorganisms produce a variety of inhibitors of PP1, which include the microcystin class of inhibitors and okadaic acid, the latter being the major cause of diarrhetic shellfish poisoning and a powerful tumor promoter. We have determined the crystal structure of the molecular complex of okadaic acid bound to PP1 to a resolution of 1.9 A. This structure reveals that the acid binds in a hydrophobic groove adjacent to the active site of the protein and interacts with basic residues within the active site. Okadaic acid exhibits a cyclic structure, which is maintained via an intramolecular hydrogen bond. This is reminiscent of other macrocyclic protein phosphatase inhibitors. The inhibitor-bound enzyme shows very little conformational change when compared with two other PP1 structures, except in the inhibitor-sensitive beta12-beta13 loop region. The selectivity of okadaic acid for protein phosphatases-1 and -2A but not PP-2B (calcineurin) may be reassessed in light of this study.


  • Organizational Affiliation

    Canadian Institutes of Health Research, Group in Protein Structure and Function, Department of Biochemistry, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT323Homo sapiensMutation(s): 0 
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P36873 (Homo sapiens)
Explore P36873 
Go to UniProtKB:  P36873
PHAROS:  P36873
GTEx:  ENSG00000186298 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36873
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OKA
Query on OKA

Download Ideal Coordinates CCD File 
E [auth A]OKADAIC ACID
C44 H68 O13
QNDVLZJODHBUFM-WFXQOWMNSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BME
Query on BME

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
OKA PDBBind:  1JK7 IC50: 3 (nM) from 1 assay(s)
BindingDB:  1JK7 IC50: min: 20, max: 5000 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.18α = 90
b = 99.18β = 90
c = 62.17γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-15
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-08-16
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description