Figure 5.

RNA recognition by RluB and RluF. (A) Comparison of RluB–RNA (blue–green and gold) that targets U2605 and RluF–RNA (gray and orange) that targets U2604. In the latter A2602 is refolded into the stem, base registry is shifted up by one base on the site 3′ of A2602, and U2604 is flipped out (11). The RNAs overlay closely in the RNA-binding grooves of the catalytic domains. (B) Representation of hydrogen bond interactions between residues of RluB and nucleotides of the RNA stem-loop. Residues that are conserved in RluF and engage in interactions with the same nucleotide (from A2590 to U2596) as RluB are highlighted in bold.