Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism

Nucleic Acids Res. 2017 Oct 13;45(18):10845-10860. doi: 10.1093/nar/gkx732.


In phylogenetically diverse bacteria, the conserved protein RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. RapZ contributes to the control of glucosamine phosphate biogenesis by selectively presenting the regulatory small RNA GlmZ to the essential ribonuclease RNase E for inactivation. Here, we report the crystal structures of full length Escherichia coli RapZ at 3.40 Å and 3.25 Å, and its isolated C-terminal domain at 1.17 Å resolution. The structural data confirm that the N-terminal domain of RapZ possesses a kinase fold, whereas the C-terminal domain bears closest homology to a subdomain of 6-phosphofructokinase, an important enzyme in the glycolytic pathway. RapZ self-associates into a domain swapped dimer of dimers, and in vivo data support the importance of quaternary structure in RNA-mediated regulation of target gene expression. Based on biochemical, structural and genetic data, we suggest a mechanism for binding and presentation by RapZ of GlmZ and the closely related decoy sRNA, GlmY. We discuss a scenario for the molecular evolution of RapZ through re-purpose of enzyme components from central metabolism.

MeSH terms

  • Amino Sugars / metabolism
  • Endoribonucleases / metabolism
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Mutation
  • Protein Binding
  • Protein Domains
  • Protein Multimerization
  • RNA / metabolism
  • RNA, Small Untranslated / metabolism
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism


  • Amino Sugars
  • Escherichia coli Proteins
  • RNA, Small Untranslated
  • RNA-Binding Proteins
  • YhbJ protein, E coli
  • RNA
  • Endoribonucleases
  • ribonuclease E