3V4Y

Crystal Structure of the first Nuclear PP1 holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.098 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Molecular Basis for Substrate Specificity of the Nuclear NIPP1:PP1 Holoenzyme.

O'Connell, N.Nichols, S.R.Heroes, E.Beullens, M.Bollen, M.Peti, W.Page, R.

(2012) Structure 20: 1746-1756

  • DOI: 10.1016/j.str.2012.08.003

  • PubMed Abstract: 
  • Regulation of protein phosphatase 1 (PP1) is controlled by a diverse array of regulatory proteins. However, how these proteins direct PP1 specificity is not well understood. More than one-third of the nuclear pool of PP1 forms a holoenzyme with the n ...

    Regulation of protein phosphatase 1 (PP1) is controlled by a diverse array of regulatory proteins. However, how these proteins direct PP1 specificity is not well understood. More than one-third of the nuclear pool of PP1 forms a holoenzyme with the nuclear inhibitor of PP1, NIPP1, to regulate chromatin remodeling, among other essential biological functions. Here, we show that the PP1-binding domain of NIPP1 is an intrinsically disordered protein, which binds PP1 in an unexpected manner. NIPP1 forms an α helix that engages PP1 at a unique interaction site, using polar rather than hydrophobic contacts. Importantly, the structure also reveals a shared PP1 interaction site outside of the RVxF motif, the ΦΦ motif. Finally, we show that NIPP1:PP1 substrate selectivity is determined by altered electrostatics and enhanced substrate localization. Together, our results provide the molecular basis by which NIPP1 directs PP1 substrate specificity in the nucleus.


    Organizational Affiliation

    Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
A, C, E, G
306Homo 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
Nuclear inhibitor of protein phosphatase 1
B, D, F, H
62Homo sapiensMutation(s): 0 
Gene Names: PPP1R8 (ARD1, NIPP1)
Find proteins for Q12972 (Homo sapiens)
Go to Gene View: PPP1R8
Go to UniProtKB:  Q12972
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C, E, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, E, G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
15P
Query on 15P

Download SDF File 
Download CCD File 
A
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.098 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.639α = 90.00
b = 116.035β = 90.00
c = 168.093γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release