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Callaghan, AJ, Aurikko, JP, Ilag, LL, Günter Grossmann, J, Chandran, V, Kühnel, K, Poljak, L, Carpousis, AJ, Robinson, CV, Symmons, MF and Luisi, BF (2004) Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J. Mol. Biol. 340:965-79

The hydrolytic endoribonuclease RNase E, which is widely distributed in bacteria and plants, plays key roles in mRNA degradation and RNA processing in Escherichia coli. The enzymatic activity of RNase E is contained within the conserved amino-terminal half of the 118 kDa protein, and the carboxy-terminal half organizes the RNA degradosome, a multi-enzyme complex that degrades mRNA co-operatively and processes ribosomal and other RNA. The study described herein demonstrates that the carboxy-terminal domain of RNase E has little structure under native conditions and is unlikely to be extensively folded within the degradosome. However, three isolated segments of 10-40 residues, and a larger fourth segment of 80 residues, are predicted to be regions of increased structural propensity. The larger of these segments appears to be a protein-RNA interaction site while the other segments possibly correspond to sites of self-recognition and interaction with the other degradosome proteins. The carboxy-terminal domain of RNase E may thus act as a flexible tether of the degradosome components. The implications of these and other observations for the organization of the RNA degradosome are discussed.

PubMed Online version:10.1016/j.jmb.2004.05.046

Amino Acid Sequence; Binding Sites; Circular Dichroism; Endoribonucleases/chemistry; Endoribonucleases/genetics; Endoribonucleases/isolation & purification; Endoribonucleases/metabolism; Escherichia coli/enzymology; Escherichia coli/genetics; Molecular Sequence Data; Multienzyme Complexes/chemistry; Multienzyme Complexes/metabolism; Phosphopyruvate Hydratase/isolation & purification; Phosphopyruvate Hydratase/metabolism; Polyribonucleotide Nucleotidyltransferase/chemistry; Polyribonucleotide Nucleotidyltransferase/metabolism; Protein Binding; Protein Structure, Tertiary; RNA Helicases/chemistry; RNA Helicases/metabolism; RNA, Bacterial/chemistry; RNA, Bacterial/metabolism; RNA-Binding Proteins/metabolism; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization