6R9J

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with A7 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.326 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases.

Tang, T.T.L.Stowell, J.A.W.Hill, C.H.Passmore, L.A.

(2019) Nat.Struct.Mol.Biol. 26: 433-442

  • DOI: 10.1038/s41594-019-0227-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 3' poly(A) tail of messenger RNA is fundamental to regulating eukaryotic gene expression. Shortening of the poly(A) tail, termed deadenylation, reduces transcript stability and inhibits translation. Nonetheless, the mechanism for poly(A) recognit ...

    The 3' poly(A) tail of messenger RNA is fundamental to regulating eukaryotic gene expression. Shortening of the poly(A) tail, termed deadenylation, reduces transcript stability and inhibits translation. Nonetheless, the mechanism for poly(A) recognition by the conserved deadenylase complexes Pan2-Pan3 and Ccr4-Not is poorly understood. Here we provide a model for poly(A) RNA recognition by two DEDD-family deadenylase enzymes, Pan2 and the Ccr4-Not nuclease Caf1. Crystal structures of Saccharomyces cerevisiae Pan2 in complex with RNA show that, surprisingly, Pan2 does not form canonical base-specific contacts. Instead, it recognizes the intrinsic stacked, helical conformation of poly(A) RNA. Using a fully reconstituted biochemical system, we show that disruption of this structure-for example, by incorporation of guanosine into poly(A)-inhibits deadenylation by both Pan2 and Caf1. Together, these data establish a paradigm for specific recognition of the conformation of poly(A) RNA by proteins that regulate gene expression.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK. passmore@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PAN2-PAN3 deadenylation complex catalytic subunit PAN2
A
672Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: PAN2
EC: 3.1.13.4
Find proteins for P53010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PAN2
Go to UniProtKB:  P53010
Entity ID: 2
MoleculeChainsLengthOrganism
A7 RNAB7Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.326 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.247 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.480α = 90.00
b = 116.409β = 90.00
c = 257.833γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council725685
Medical Research Council (United Kingdom)United KingdomMC_U105192715

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references
  • Version 1.2: 2019-06-19
    Type: Data collection, Database references
  • Version 1.3: 2019-08-21
    Type: Data collection