4MOY

Structure of a second nuclear PP1 Holoenzyme, crystal form 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1953 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Understanding the antagonism of retinoblastoma protein dephosphorylation by PNUTS provides insights into the PP1 regulatory code.

Choy, M.S.Hieke, M.Kumar, G.S.Lewis, G.R.Gonzalez-Dewhitt, K.R.Kessler, R.P.Stein, B.J.Hessenberger, M.Nairn, A.C.Peti, W.Page, R.

(2014) Proc.Natl.Acad.Sci.USA 111: 4097-4102

  • DOI: 10.1073/pnas.1317395111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. However, how these proteins direct PP1 specificity and the ab ...

    The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. However, how these proteins direct PP1 specificity and the ability to predict how these PP1 interacting proteins bind PP1 from sequence alone is still missing. PP1 nuclear targeting subunit (PNUTS) is a PP1 targeting protein that, with PP1, plays a central role in the nucleus, where it regulates chromatin decondensation, RNA processing, and the phosphorylation state of fundamental cell cycle proteins, including the retinoblastoma protein (Rb), p53, and MDM2. The molecular function of PNUTS in these processes is completely unknown. Here, we show that PNUTS, which is intrinsically disordered in its free form, interacts strongly with PP1 in a highly extended manner. Unexpectedly, PNUTS blocks one of PP1's substrate binding grooves while leaving the active site accessible. This interaction site, which we have named the arginine site, allowed us to define unique PP1 binding motifs, which advances our ability to predict how more than a quarter of the known PP1 regulators bind PP1. Additionally, the structure shows how PNUTS inhibits the PP1-mediated dephosphorylation of critical substrates, especially Rb, by blocking their binding sites on PP1, insights that are providing strategies for selectively enhancing Rb activity.


    Organizational Affiliation

    Departments of Molecular Pharmacology, Physiology, and Biotechnology, Molecular Biology, Cell Biology, and Biochemistry, and Chemistry, Brown University, Providence, RI 02912.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
A
299Homo sapiensMutation(s): 0 
Gene Names: PPP1CA (PPP1A)
EC: 3.1.3.16
Find proteins for P62136 (Homo sapiens)
Go to Gene View: PPP1CA
Go to UniProtKB:  P62136
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 1 regulatory subunit 10
B
44Rattus norvegicusMutation(s): 0 
Gene Names: Ppp1r10 (Cat53, Pnuts)
Find proteins for O55000 (Rattus norvegicus)
Go to UniProtKB:  O55000
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1953 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.788α = 90.00
b = 130.788β = 90.00
c = 47.725γ = 120.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXphasing
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Database references