4JZV

Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - second guanosine residue in guanosine binding pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.

Piton, J.Larue, V.Thillier, Y.Dorleans, A.Pellegrini, O.Li de la Sierra-Gallay, I.Vasseur, J.J.Debart, F.Tisne, C.Condon, C.

(2013) Proc Natl Acad Sci U S A 110: 8858-8863

  • DOI: https://doi.org/10.1073/pnas.1221510110
  • Primary Citation of Related Structures:  
    4JZS, 4JZT, 4JZU, 4JZV

  • PubMed Abstract: 

    The initiation of mRNA degradation often requires deprotection of its 5' end. In eukaryotes, the 5'-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5'-monophosphorylated RNA that is a substrate for 5' exoribonucleases. In bacteria, the 5'-triphosphate group of primary transcripts is also converted to a 5' monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5' exoribonucleases. Here we present the crystal structures of Bacillus subtilis RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to Bdellovibrio bacteriovorus RppH, which recognizes the first nucleotide of its RNA targets, the B. subtilis enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria.


  • Organizational Affiliation

    Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA PYROPHOSPHOHYDROLASE
A, B
158Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU30630mutTAytkD
EC: 3.6.1.55
UniProt
Find proteins for O35013 (Bacillus subtilis (strain 168))
Explore O35013 
Go to UniProtKB:  O35013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35013
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*(GCP)P*G)-3')2N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.158α = 90
b = 138.025β = 90
c = 35.684γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description