7SOY

The structure of the PP2A-B56gamma1 holoenzyme-PME-1 complex

• PDB DOI:  https://doi.org/10.2210/pdb7SOY/pdb
• EM Map EMD-25363: EMDB EMDataResource

• Classification: RECOMBINATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2021-11-01 Released: 2022-08-31 
• Deposition Author(s): Li, Y., Balakrishnan, V.K., Rowse, M., Novikova, I.V., Xing, Y.
• Funding Organization(s): American Cancer Society, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition.

Li, Y., Balakrishnan, V.K., Rowse, M., Wu, C.G., Bravos, A.P., Yadav, V.K., Ivarsson, Y., Strack, S., Novikova, I.V., Xing, Y.

(2022) Elife 11

• PubMed: 35924897 
• DOI: https://doi.org/10.7554/eLife.79736
• Primary Citation of Related Structures:  
  7SOY


• PubMed Abstract: 
  

Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme-PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.

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Related Citations: 

• Real-space refinement in PHENIX for cryo-EM and crystallography
  Xing, Y.
  (2018) Acta Crystallogr D Biol Crystallogr 74: 531

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Organizational Affiliation: 

Biophysics program, University of Wisconsin at Madison, Madison, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 196.06 kDa 
• Atom Count: 12,180 
• Modelled Residue Count: 1,529 
• Deposited Residue Count: 1,733 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	A	589	Homo sapiens	Mutation(s): 0  Gene Names: PPP2R1A
UniProt & NIH Common Fund Data Resources
Find proteins for P30153 (Homo sapiens) Explore P30153  Go to UniProtKB:  P30153
PHAROS:  P30153

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Gamma-1 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform	B	449	Homo sapiens	Mutation(s): 0  Gene Names: PPP2R5C, KIAA0044
UniProt & NIH Common Fund Data Resources
Find proteins for Q13362 (Homo sapiens) Explore Q13362  Go to UniProtKB:  Q13362
PHAROS:  Q13362

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	C	309	Homo sapiens	Mutation(s): 0  Gene Names: PPP2CA EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P67775 (Homo sapiens) Explore P67775  Go to UniProtKB:  P67775
PHAROS:  P67775

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase methylesterase 1	D [auth P]	386	Homo sapiens	Mutation(s): 1  Gene Names: PPME1, PME1, PP2593, PRO0750 EC: 3.1.1.89
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y570 (Homo sapiens) Explore Q9Y570  Go to UniProtKB:  Q9Y570
PHAROS:  Q9Y570

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Li, Y., Balakrishnan, V.K., Rowse, M., Novikova, I.V., Xing, Y.

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Funding Organization	Location	Grant Number
American Cancer Society		RSG-10-153-01-DMC
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		R01 GM096060-01
Other private		A19-3376-5007

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release