4OJJ

Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator (Space group : P212121)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The C-terminal domain from S. cerevisiae Pat1 displays two conserved regions involved in decapping factor recruitment.

Fourati, Z.Kolesnikova, O.Back, R.Keller, J.Charenton, C.Taverniti, V.Plesse, C.G.Lazar, N.Durand, D.van Tilbeurgh, H.Seraphin, B.Graille, M.

(2014) PLoS One 9: e96828-e96828

  • DOI: 10.1371/journal.pone.0096828
  • Primary Citation of Related Structures:  
    4OGP, 4OJJ

  • PubMed Abstract: 
  • Eukaryotic mRNA decay is a highly regulated process allowing cells to rapidly modulate protein production in response to internal and environmental cues. Mature translatable eukaryotic mRNAs are protected from fast and uncontrolled degradation in the cytoplasm by two cis-acting stability determinants: a methylguanosine (m(7)G) cap and a poly(A) tail at their 5' and 3' extremities, respectively ...

    Eukaryotic mRNA decay is a highly regulated process allowing cells to rapidly modulate protein production in response to internal and environmental cues. Mature translatable eukaryotic mRNAs are protected from fast and uncontrolled degradation in the cytoplasm by two cis-acting stability determinants: a methylguanosine (m(7)G) cap and a poly(A) tail at their 5' and 3' extremities, respectively. The hydrolysis of the m(7)G cap structure, known as decapping, is performed by the complex composed of the Dcp2 catalytic subunit and its partner Dcp1. The Dcp1-Dcp2 decapping complex has a low intrinsic activity and requires accessory factors to be fully active. Among these factors, Pat1 is considered to be a central scaffolding protein involved in Dcp2 activation but also in inhibition of translation initiation. Here, we present the structural and functional study of the C-terminal domain from S. cerevisiae Pat1 protein. We have identified two conserved and functionally important regions located at both extremities of the domain. The first region is involved in binding to Lsm1-7 complex. The second patch is specific for fungal proteins and is responsible for Pat1 interaction with Edc3. These observations support the plasticity of the protein interaction network involved in mRNA decay and show that evolution has extended the C-terminal alpha-helical domain from fungal Pat1 proteins to generate a new binding platform for protein partners.


    Organizational Affiliation

    Laboratoire de Biochimie, Centre National de Recherche Scientifique (CNRS) UMR 7654, Ecole Polytechnique, Palaiseau Cedex, France; Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC), Centre National de Recherche Scientifique (CNRS) UMR 8619, Bat. 430, Université Paris Sud, Orsay Cedex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 2-associated protein PAT1B [auth A],
C [auth B],
A [auth C]
330Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAT1MRT1YCR077CYCR77C
UniProt
Find proteins for P25644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25644 
Go to UniProtKB:  P25644
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25644
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.43α = 90
b = 173.54β = 90
c = 175.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Structure summary