Structures of RNA complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5'-end-dependent mRNA decay

J Biol Chem. 2015 Apr 10;290(15):9487-99. doi: 10.1074/jbc.M114.634824. Epub 2015 Feb 5.


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.

Keywords: Crystal Structure; Hydrolase; RNA Degradation; RNA Structure; RNA-Protein Interaction; RNA-binding Protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acid Anhydride Hydrolases / chemistry*
  • Acid Anhydride Hydrolases / genetics
  • Acid Anhydride Hydrolases / metabolism
  • Amino Acid Sequence
  • Apoenzymes / chemistry
  • Apoenzymes / genetics
  • Apoenzymes / metabolism
  • Bacillus subtilis / enzymology
  • Bacillus subtilis / genetics
  • Binding Sites / genetics
  • Biocatalysis
  • Crystallography, X-Ray
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Hydrogen Bonding
  • Magnesium / chemistry
  • Magnesium / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA Stability*
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • Sequence Homology, Amino Acid
  • Species Specificity
  • Substrate Specificity


  • Apoenzymes
  • Escherichia coli Proteins
  • RNA, Bacterial
  • Acid Anhydride Hydrolases
  • RppH protein, E coli
  • Magnesium

Associated data

  • PDB/4S2V
  • PDB/4S2W
  • PDB/4S2X
  • PDB/4S2Y