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The solution structure of ribosomal protein S4 Δ41 reveals two subdomains and a positively charged surface that may interact with RNA
Author(s) -
Markus Michelle A.,
Gerstner Resi B.,
Draper David E.,
Torchia Dennis A.
Publication year - 1998
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/17.16.4559
Subject(s) - rna , biology , antiparallel (mathematics) , ribosome , pseudoknot , heteronuclear molecule , ribosomal rna , biophysics , heteronuclear single quantum coherence spectroscopy , nucleic acid structure , operon , stem loop , crystallography , nuclear magnetic resonance spectroscopy , biochemistry , physics , stereochemistry , chemistry , gene , escherichia coli , quantum mechanics , magnetic field
S4 is one of the first proteins to bind to 16S RNA during assembly of the prokaryotic ribosome. Residues 43–200 of S4 from Bacillus stearothermophilus (S4 Δ41) bind specifically to both 16S rRNA and to a pseudoknot within the α operon mRNA. As a first step toward understanding how S4 recognizes and organizes RNA, we have solved the structure of S4 Δ41 in solution by multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The fold consists of two globular subdomains, one comprised of four helices and the other comprised of a five‐stranded antiparallel β‐sheet and three helices. Although cross‐linking studies suggest that residues between helices α2 and α3 are close to RNA, the concentration of positive charge along the crevice between the two subdomains suggests that this could be an RNA‐binding site. In contrast to the L11 RNA‐binding domain studied previously, S4 Δ41 shows no fast local motions, suggesting that it has less capacity for refolding to fit RNA. The independently determined crystal structure of S4 Δ41 shows similar features, although there is small rotation of the subdomains compared with the solution structure. The relative orientation of the subdomains in solution will be verified with further study.