4I5N

Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Ca(2+)-dependent PP2A heterotrimer and insights into Cdc6 dephosphorylation.

Wlodarchak, N.Guo, F.Satyshur, K.A.Jiang, L.Jeffrey, P.D.Sun, T.Stanevich, V.Mumby, M.C.Xing, Y.

(2013) Cell Res 23: 931-946

  • DOI: 10.1038/cr.2013.77
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The B″/PR72 family of protein phosphatase 2A (PP2A) is an important PP2A family involved in diverse cellular processes, and uniquely regulated by calcium binding to the regulatory subunit. The PR70 subunit in this family interacts with cell division ...

    The B″/PR72 family of protein phosphatase 2A (PP2A) is an important PP2A family involved in diverse cellular processes, and uniquely regulated by calcium binding to the regulatory subunit. The PR70 subunit in this family interacts with cell division control 6 (Cdc6), a cell cycle regulator important for control of DNA replication. Here, we report crystal structures of the isolated PR72 and the trimeric PR70 holoenzyme at a resolution of 2.1 and 2.4 Å, respectively, and in vitro characterization of Cdc6 dephosphorylation. The holoenzyme structure reveals that one of the PR70 calcium-binding motifs directly contacts the scaffold subunit, resulting in the most compact scaffold subunit conformation among all PP2A holoenzymes. PR70 also binds distinctively to the catalytic subunit near the active site, which is required for PR70 to enhance phosphatase activity toward Cdc6. Our studies provide a structural basis for unique regulation of B″/PR72 holoenzymes by calcium ions, and suggest the mechanisms for precise control of substrate specificity among PP2A holoenzymes.


    Organizational Affiliation

    McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
A, D
584Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
Find proteins for P30153 (Homo sapiens)
Go to UniProtKB:  P30153
NIH Common Fund Data Resources
PHAROS  P30153
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct
B, E
413Homo sapiensMutation(s): 0 
Gene Names: PPP2R3BPPP2R3L
Find proteins for Q99741 (Homo sapiens)
Go to UniProtKB:  Q99741
NIH Common Fund Data Resources
PHAROS  Q99741
Find proteins for Q9Y5P8 (Homo sapiens)
Go to UniProtKB:  Q9Y5P8
NIH Common Fund Data Resources
PHAROS  Q9Y5P8
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha
C, F
311Homo sapiensMutation(s): 0 
Gene Names: PPP2CA
EC: 3.1.3.16
Find proteins for P67775 (Homo sapiens)
Go to UniProtKB:  P67775
NIH Common Fund Data Resources
PHAROS  P67775
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Microcystin-LR (MCLR) bound form
G, H
7Microcystis aeruginosaMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
C, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001031
Query on PRD_001031
G, HMicrocystin-LR (MCLR) bound formOligopeptide /  Toxin

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
MAA
Query on MAA
G,HL-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.1α = 90
b = 101.077β = 90
c = 347.164γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CRANKphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Structure summary
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2017-08-09
    Changes: Advisory, Data collection, Refinement description, Source and taxonomy