4S2Y

Structure of E. coli RppH bound to RNA and three magnesium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay.

Vasilyev, N.Serganov, A.

(2015) J Biol Chem 290: 9487-9499

  • DOI: 10.1074/jbc.M114.634824
  • Primary Citation of Related Structures:  
    4S2V, 4S2W, 4S2X, 4S2Y

  • PubMed Abstract: 
  • 5'-End-dependent RNA degradation impacts virulence, stress responses, and DNA repair in bacteria by controlling the decay of hundreds of mRNAs. The RNA pyrophosphohydrolase RppH, a member of the Nudix hydrolase superfamily, triggers this degradation ...

    5'-End-dependent RNA degradation impacts virulence, stress responses, and DNA repair in bacteria by controlling the decay of hundreds of mRNAs. The RNA pyrophosphohydrolase RppH, a member of the Nudix hydrolase superfamily, triggers this degradation pathway by removing pyrophosphate from the triphosphorylated RNA 5' terminus. Here, we report the x-ray structures of Escherichia coli RppH (EcRppH) in apo- and RNA-bound forms. These structures show distinct conformations of EcRppH·RNA complexes on the catalytic pathway and suggest a common catalytic mechanism for Nudix hydrolases. EcRppH interacts with RNA by a bipartite mechanism involving specific recognition of the 5'-terminal triphosphate and the second nucleotide, thus enabling discrimination against mononucleotides as substrates. The structures also reveal the molecular basis for the preference of the enzyme for RNA substrates bearing guanine in the second position by identifying a protein cleft in which guanine interacts with EcRppH side chains via cation-π contacts and hydrogen bonds. These interactions explain the modest specificity of EcRppH at the 5' terminus and distinguish the enzyme from the highly selective RppH present in Bacillus subtilis. The divergent means by which RNA is recognized by these two functionally and structurally analogous enzymes have important implications for mRNA decay and the regulation of protein biosynthesis in bacteria.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016 alexander.serganov@nyumc.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA pyrophosphohydrolaseA161Escherichia coli K-12Mutation(s): 2 
Gene Names: rppHnudHygdPb2830JW2798
EC: 3.6.1
Find proteins for P0A776 (Escherichia coli (strain K12))
Explore P0A776 
Go to UniProtKB:  P0A776
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*(APC)*GP*U)-3')B3N/A
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download CCD File 
    A
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    CL
    Query on CL

    Download CCD File 
    A
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A, B
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.60 Å
    • R-Value Free: 0.199 
    • R-Value Work: 0.172 
    • R-Value Observed: 0.173 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 79.631α = 90
    b = 36.484β = 102.3
    c = 58.073γ = 90
    Software Package:
    Software NamePurpose
    CrystalCleardata collection
    PHENIXmodel building
    PHENIXrefinement
    XDSdata reduction
    XDSdata scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2015-02-11
      Type: Initial release
    • Version 1.1: 2015-02-25
      Changes: Database references
    • Version 1.2: 2015-05-06
      Changes: Database references