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The 23 S rRNA environment of ribosomal protein L9 in the 50 S ribosomal subunit.

Authors
  • Kr, Lieberman
  • Ma, Firpo
  • Aj, Herr
  • T, Nguyenle
  • Jf, Atkins
  • Rf, Gesteland
  • Harry Noller
Type
Published Article
Journal
Journal of Molecular Biology
Publisher
Elsevier
Volume
297
Issue
5
Pages
1129–1143
Source
UCSC Bioinformatics biomedical-ucsc
License
Unknown

Abstract

Ribosomal protein L9 consists of two globular alpha/beta domains separated by a nine-turn alpha-helix. We examined the rRNA environment of L9 by chemical footprinting and directed hydroxyl radical probing. We reconstituted L9, or individual domains of L9, with L9-deficient 50 S subunits, or with deproteinized 23 S rRNA. A footprint was identified in domain V of 23 S rRNA that was mainly attributable to N-domain binding. Fe(II) was tethered to L9 via cysteine residues introduced at positions along the alpha-helix and in the C-domain, and derivatized proteins were reconstituted with L9-deficient subunits. Directed hydroxyl radical probing targeted regions of domains I, III, IV, and V of 23 S rRNA, reinforcing the view that 50 S subunit architecture is typified by interwoven rRNA domains. There was a striking correlation between the cleavage patterns from the Fe(II) probes attached to the alpha-helix and their predicted orientations, constraining both the position and orientation of L9, as well as the arrangement of specific elements of 23 S rRNA, in the 50 S subunit.

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