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

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

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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: https://doi.org/10.1038/s41594-019-0227-9
  • Primary Citation of Related Structures:  
    6R9I, 6R9J, 6R9M, 6R9O, 6R9P, 6R9Q

  • 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) 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PAN2-PAN3 deadenylation complex catalytic subunit PAN2672Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: PAN2YGL094C
Find proteins for P53010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53010 
Go to UniProtKB:  P53010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53010
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.373α = 90
b = 117.075β = 90
c = 255.319γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-08-21
    Changes: Data collection
  • Version 1.4: 2020-01-29
    Changes: Data collection
  • Version 1.5: 2024-01-24
    Changes: Data collection, Database references, Refinement description