3C5W

Complex between PP2A-specific methylesterase PME-1 and PP2A core enzyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural mechanism of demethylation and inactivation of protein phosphatase 2A.

Xing, Y., Li, Z., Chen, Y., Stock, J.B., Jeffrey, P.D., Shi, Y.

(2008) Cell 133: 154-163

  • DOI: 10.1016/j.cell.2008.02.041
  • Primary Citation of Related Structures:  
    3C5V, 3C5W

  • PubMed Abstract: 

    • Protein phosphatase 2A (PP2A) is an important serine/threonine phosphatase that plays a role in many biological processes. Reversible carboxyl methylation of the PP2A catalytic subunit is an essential regulatory mechanism for its function. Demethylation ...

    Protein phosphatase 2A (PP2A) is an important serine/threonine phosphatase that plays a role in many biological processes. Reversible carboxyl methylation of the PP2A catalytic subunit is an essential regulatory mechanism for its function. Demethylation and negative regulation of PP2A is mediated by a PP2A-specific methylesterase PME-1, which is conserved from yeast to humans. However, the underlying mechanism of PME-1 function remains enigmatic. Here we report the crystal structures of PME-1 by itself and in complex with a PP2A heterodimeric core enzyme. The structures reveal that PME-1 directly binds to the active site of PP2A and that this interaction results in the activation of PME-1 by rearranging the catalytic triad into an active conformation. Strikingly, these interactions also lead to inactivation of PP2A by evicting the manganese ions that are required for the phosphatase activity of PP2A. These observations identify a dual role of PME-1 that regulates PP2A activation, methylation, and holoenzyme assembly in cells.

    Organizational Affiliation: 

    Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ 08544, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PP2A A subunit A232Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
Find proteins for P30153 (Homo sapiens)
Explore P30153 
Go to UniProtKB:  P30153
NIH Common Fund Data Resources
PHAROS:  P30153
GTEx:  ENSG00000105568
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PP2A C subunit C310Homo sapiensMutation(s): 0 
Gene Names: PPP2CA
EC: 3.1.3.16
Find proteins for P67775 (Homo sapiens)
Explore P67775 
Go to UniProtKB:  P67775
NIH Common Fund Data Resources
PHAROS:  P67775
GTEx:  ENSG00000113575
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PP2A-specific methylesterase PME-1 P310Homo sapiensMutation(s): 0 
Gene Names: PPME1
EC: 3.1.1.89
Find proteins for Q9Y570 (Homo sapiens)
Explore Q9Y570 
Go to UniProtKB:  Q9Y570
NIH Common Fund Data Resources
PHAROS:  Q9Y570
GTEx:  ENSG00000214517
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.292α = 90
b = 54.839β = 110.87
c = 125.146γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Source and taxonomy