3V4Y

Crystal Structure of the first Nuclear PP1 holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: https://doi.org/10.1016/j.str.2012.08.003
  • Primary Citation of Related Structures:  
    3V4Y

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
A, C, E, G
306Homo sapiensMutation(s): 0 
Gene Names: PPP1APPP1CA
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear inhibitor of protein phosphatase 1
B, D, F, H
62Homo sapiensMutation(s): 0 
Gene Names: PPP1R8ARD1NIPP1
EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q12972 (Homo sapiens)
Explore Q12972 
Go to UniProtKB:  Q12972
PHAROS:  Q12972
GTEx:  ENSG00000117751 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12972
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
N [auth A]POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth G]
K [auth A]
L [auth A]
M [auth A]
Q [auth C]
AA [auth G],
K [auth A],
L [auth A],
M [auth A],
Q [auth C],
R [auth C],
S [auth C],
V [auth E],
W [auth E],
X [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
O [auth C]
P [auth C]
T [auth E]
I [auth A],
J [auth A],
O [auth C],
P [auth C],
T [auth E],
U [auth E],
Y [auth G],
Z [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.639α = 90
b = 116.035β = 90
c = 168.093γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations