8U89

The structure of the PP2A-B56Delta holoenzyme mutant - E197K

  • Classification: CELL CYCLE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): Yes 

  • Deposited: 2023-09-16 Released: 2024-01-10 
  • Deposition Author(s): Wu, C.G., Xing, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

B56 delta long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations.

Wu, C.G.Balakrishnan, V.K.Merrill, R.A.Parihar, P.S.Konovolov, K.Chen, Y.C.Xu, Z.Wei, H.Sundaresan, R.Cui, Q.Wadzinski, B.E.Swingle, M.R.Musiyenko, A.Chung, W.K.Honkanen, R.E.Suzuki, A.Huang, X.Strack, S.Xing, Y.

(2024) Proc Natl Acad Sci U S A 121: e2310727120-e2310727120

  • DOI: https://doi.org/10.1073/pnas.2310727120
  • Primary Citation of Related Structures:  
    8U1X, 8U89

  • PubMed Abstract: 

    Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D ) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.


  • Organizational Affiliation

    McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI 53705.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform589Homo sapiensMutation(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
GTEx:  ENSG00000105568 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30153
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform602Homo sapiensMutation(s): 1 
Gene Names: PPP2R5D
UniProt & NIH Common Fund Data Resources
Find proteins for Q14738 (Homo sapiens)
Explore Q14738 
Go to UniProtKB:  Q14738
PHAROS:  Q14738
GTEx:  ENSG00000112640 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14738
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform309Homo sapiensMutation(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
GTEx:  ENSG00000113575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67775
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM137090-01

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release