6DNO | pdb_00006dno

Crystal structure of Protein Phosphatase 1 (PP1) bound to the muscle glycogen-targeting subunit (Gm)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6DNO

This is version 2.0 of the entry. See complete history

Literature

Identification of the substrate recruitment mechanism of the muscle glycogen protein phosphatase 1 holoenzyme.

Kumar, G.S.Choy, M.S.Koveal, D.M.Lorinsky, M.K.Lyons, S.P.Kettenbach, A.N.Page, R.Peti, W.

(2018) Sci Adv 4: eaau6044-eaau6044

  • DOI: https://doi.org/10.1126/sciadv.aau6044
  • Primary Citation Related Structures: 
    6DNO

  • PubMed Abstract: 

    Glycogen is the primary storage form of glucose. Glycogen synthesis and breakdown are tightly controlled by glycogen synthase (GYS) and phosphorylase, respectively. The enzyme responsible for dephosphorylating GYS and phosphorylase, which results in their activation (GYS) or inactivation (phosphorylase) to robustly stimulate glycogen synthesis, is protein phosphatase 1 (PP1). However, our understanding of how PP1 recruits these substrates is limited. Here, we show how PP1, together with its muscle glycogen-targeting (G M ) regulatory subunit, recruits and selectively dephosphorylates its substrates. Our molecular data reveal that the G M carbohydrate binding module (G M CBM21 ), which is amino-terminal to the G M PP1 binding domain, has a dual function in directing PP1 substrate specificity: It either directly recruits substrates (i.e., GYS) or recruits them indirectly by localization (via glycogen for phosphorylase). Our data provide the molecular basis for PP1 regulation by G M and reveal how PP1-mediated dephosphorylation is driven by scaffolding-based substrate recruitment.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.

Macromolecule Content 

  • Total Structure Weight: 38.63 kDa 
  • Atom Count: 2,781 
  • Modeled Residue Count: 323 
  • Deposited Residue Count: 336 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit299Homo sapiensMutation(s): 0 
Gene Names: PPP1CAPPP1A
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P62136 (Homo sapiens)
Explore P62136 
Go to UniProtKB:  P62136
PHAROS:  P62136
GTEx:  ENSG00000172531 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62136
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein phosphatase 1 regulatory subunit 3A30Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for Q00756 (Oryctolagus cuniculus)
Explore Q00756 
Go to UniProtKB:  Q00756
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00756
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Microcystin-LR7synthetic constructMutation(s): 0 

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.476α = 90
b = 65.744β = 90
c = 160.355γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesGM098482
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesNS091336

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations