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Identification of the ribosome binding sites of translation initiation factor IF3 by multidimensional heteronuclear NMR spectroscopy

Published online by Cambridge University Press:  01 January 1999

MARCO SETTE
Affiliation:
Department of Chemical Sciences and Technology, University of Rome “Tor Vergata,” 00133, Rome, Italy Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
ROBERTO SPURIO
Affiliation:
Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032, Camerino, Italy
PAUL VAN TILBORG
Affiliation:
Department of Chemical Sciences and Technology, University of Rome “Tor Vergata,” 00133, Rome, Italy
CLAUDIO O. GUALERZI
Affiliation:
Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032, Camerino, Italy
ROLF BOELENS
Affiliation:
Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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Abstract

Titrations of Escherichia coli translation initiation factor IF3, isotopically labeled with 15N, with 30S ribosomal subunits were followed by NMR by recording two-dimensional (15N,1H)-HSQC spectra. In the titrations, intensity changes are observed for cross peaks belonging to amides of individual amino acids. At low concentrations of ribosomal subunits, only resonances belonging to amino acids of the C-domain of IF3 are affected, whereas all those attributed to the N-domain are still visible. Upon addition of a larger amount of 30S subunits cross peaks belonging to residues of the N-terminal domain of the protein are also selectively affected.

Our results demonstrate that the two domains of IF3 are functionally independent, each interacting with a different affinity with the ribosomal subunits, thus allowing the identification of the individual residues of the two domains involved in this interaction. Overall, the C-domain interacts with the 30S subunits primarily through some of its loops and α-helices and the residues involved in ribosome binding are distributed rather symmetrically over a fairly large surface of the domain, while the N-domain interacts mainly via a small number of residues distributed asymmetrically in this domain.

The spatial organization of the active sites of IF3, emerging through the comparison of the present data with the previous chemical modification and mutagenesis data, is discussed in light of the ribosomal localization of IF3 and of the mechanism of action of this factor.

Type
Research Article
Copyright
© 1999 RNA Society

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