6ZEG

Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme.

Fedoryshchak, R.O.Prechova, M.Butler, A.Lee, R.O'Reilly, N.Flynn, H.R.Snijders, A.P.Eder, N.Ultanir, S.Mouilleron, S.Treisman, R.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.61509
  • Primary Citation of Related Structures:  
    6ZEE, 6ZEF, 6ZEG, 6ZEH, 6ZEI, 6ZEJ

  • PubMed Abstract: 

    PPP-family phosphatases such as PP1 have little intrinsic specificity. Cofactors can target PP1 to substrates or subcellular locations, but it remains unclear how they might confer sequence-specificity on PP1. The cytoskeletal regulator Phactr1 is a neuronally enriched PP1 cofactor that is controlled by G-actin. Structural analysis showed that Phactr1 binding remodels PP1's hydrophobic groove, creating a new composite surface adjacent to the catalytic site. Using phosphoproteomics, we identified mouse fibroblast and neuronal Phactr1/PP1 substrates, which include cytoskeletal components and regulators. We determined high-resolution structures of Phactr1/PP1 bound to the dephosphorylated forms of its substrates IRSp53 and spectrin αII. Inversion of the phosphate in these holoenzyme-product complexes supports the proposed PPP-family catalytic mechanism. Substrate sequences C-terminal to the dephosphorylation site make intimate contacts with the composite Phactr1/PP1 surface, which are required for efficient dephosphorylation. Sequence specificity explains why Phactr1/PP1 exhibits orders-of-magnitude enhanced reactivity towards its substrates, compared to apo-PP1 or other PP1 holoenzymes.


  • Organizational Affiliation

    Signalling and Transcription Laboratory, The Francis Crick Institute, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis inhibitor 1-associated protein 2A,
C [auth B]
338Homo sapiensMutation(s): 0 
Gene Names: PPP1CAPPP1ABAIAP2
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQB8 (Homo sapiens)
Explore Q9UQB8 
Go to UniProtKB:  Q9UQB8
PHAROS:  Q9UQB8
GTEx:  ENSG00000175866 
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 GroupsP62136Q9UQB8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatase and actin regulatorB [auth C],
D
70Homo sapiensMutation(s): 0 
Gene Names: PHACTR1hCG_1818446
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0D0 (Homo sapiens)
Explore Q9C0D0 
Go to UniProtKB:  Q9C0D0
PHAROS:  Q9C0D0
GTEx:  ENSG00000112137 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C0D0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
16P
Query on 16P

Download Ideal Coordinates CCD File 
M [auth B]3,6,9,12,15,18-HEXAOXAICOSANE
C14 H30 O6
IXFAFGFZFQHRLB-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.616α = 90
b = 122.394β = 92.219
c = 69.097γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description