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 1.0 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
  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunitA, C, E, G306Homo sapiensMutation(s): 0 
Gene Names: PPP1APPP1CA
EC: 3.1.3.16
Find proteins for P62136 (Homo sapiens)
Explore P62136 
Go to UniProtKB:  P62136
NIH Common Fund Data Resources
PHAROS:  P62136
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear inhibitor of protein phosphatase 1B, D, F, H62Homo sapiensMutation(s): 0 
Gene Names: PPP1R8ARD1NIPP1
EC: 3.1.4
Find proteins for Q12972 (Homo sapiens)
Explore Q12972 
Go to UniProtKB:  Q12972
NIH Common Fund Data Resources
PHAROS:  Q12972
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth G] , K [auth A] , L [auth A] , M [auth A] , Q [auth C] , R [auth C] , S [auth C] , V [auth E] , 
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
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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