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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.

Original publication

DOI

10.1021/bi0351099

Type

Journal article

Journal

Biochemistry

Publication Date

02/12/2003

Volume

42

Pages

13848 - 13855

Keywords

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