Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)

Experimental Data Snapshot

  • Resolution: 3.17 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.283 

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Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis.

Leroy, M.Piton, J.Gilet, L.Pellegrini, O.Proux, C.Coppee, J.Y.Figaro, S.Condon, C.

(2017) EMBO J 36: 1167-1181

  • DOI: https://doi.org/10.15252/embj.201796540
  • Primary Citation of Related Structures:  
    5MQ8, 5MQ9

  • PubMed Abstract: 

    The PIN domain plays a central role in cellular RNA biology and is involved in processes as diverse as rRNA maturation, mRNA decay and telomerase function. Here, we solve the crystal structure of the Rae1 (YacP) protein of Bacillus subtilis , a founding member of the NYN (Nedd4-BP1/YacP nuclease) subfamily of PIN domain proteins, and identify potential substrates in vivo Unexpectedly, degradation of a characterised target mRNA was completely dependent on both its translation and reading frame. We provide evidence that Rae1 associates with the B. subtilis ribosome and cleaves between specific codons of this mRNA in vivo Critically, we also demonstrate translation-dependent Rae1 cleavage of this substrate in a purified translation assay in vitro Multiple lines of evidence converge to suggest that Rae1 is an A-site endoribonuclease. We present a docking model of Rae1 bound to the B. subtilis ribosomal A-site that is consistent with this hypothesis and show that Rae1 cleaves optimally immediately upstream of a lysine codon (AAA or AAG) in vivo .

  • Organizational Affiliation

    UMR 8261 (CNRS - Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YacP
A, B
181Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: yacPBSU00970
Find proteins for P37574 (Bacillus subtilis (strain 168))
Explore P37574 
Go to UniProtKB:  P37574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37574
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.17 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.283 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.7α = 90
b = 63.95β = 90
c = 138.43γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection