Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain

Biochemistry. 2003 Dec 2;42(47):13848-55. doi: 10.1021/bi0351099.

Abstract

RNase E is an essential endoribonuclease that plays a central role in the processing and degradation of RNA in Escherichia coli and other bacteria. Most endoribonucleases have been shown to act distributively; however, Feng et al. [(2002) Proc. Natl. Acad. Sci. U.S.A. 99, 14746-14751] have recently found that RNase E acts via a scanning mechanism. A structural explanation for the processivity of RNase E is provided here, with our finding that the conserved catalytic domain of E. coli RNase E forms a homotetramer. Nondissociating nanoflow-electrospray mass spectrometry suggests that the tetramer binds up to four molecules of a specific substrate RNA analogue. The tetrameric assembly of the N-terminal domain of RNase E is consistent with crystallographic analyses, which indicate that the tetramer possesses approximate D(2) dihedral symmetry. Using X-ray solution scattering data and symmetry restraints, a solution shape is calculated for the tetramer. This shape, together with limited proteolysis data, suggests that the S1-RNA binding domains of RNase E lie on the periphery of the tetramer. These observations have implications for the structure and function of the RNase E/RNase G ribonuclease family and for the assembly of the E. coli RNA degradosome, in which RNase E is the central component.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Catalysis
  • Catalytic Domain*
  • Chymotrypsin / chemistry
  • Crystallization
  • Endoribonucleases / chemistry*
  • Escherichia coli Proteins / chemistry*
  • Hydrolysis
  • Models, Molecular
  • Molecular Sequence Data
  • Multienzyme Complexes / chemistry
  • Nanotechnology
  • Peptide Fragments / chemistry*
  • Polyribonucleotide Nucleotidyltransferase / chemistry
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • RNA Helicases / chemistry
  • Recombinant Proteins / chemistry
  • Scattering, Radiation
  • Spectrometry, Mass, Electrospray Ionization
  • X-Rays

Substances

  • Escherichia coli Proteins
  • Multienzyme Complexes
  • Peptide Fragments
  • Recombinant Proteins
  • degradosome
  • Polyribonucleotide Nucleotidyltransferase
  • Endoribonucleases
  • ribonuclease E
  • Chymotrypsin
  • RNA Helicases

Associated data

  • PDB/2A8V