Figure 4.

Sa Hfq does not utilize an A-site to bind A-rich RNA. (A) Overlay of Sa Hfq–A₄ and Ec Hfq–A₁₅ complex structures. Key side chains are shown as sticks and labeled for Sa Hfq. The carbon atoms of the Sa Hfq side chains are colored grey whereas the carbon atoms of the Ec Hfq side chains are colored magenta. The Ec Hfq A-site and the Sa Hfq L-site adenosines are shown in thick magenta and grey sticks, respectively, whereas the rest of the respective RNAs is shown in thin magenta and grey lines. Black double-headed lines indicate steric clash between the A-site adenosine and side chains of Sa Hfq and the distances in Angstrom are shown. The locations of the respective R-site, A-site and L-site are labeled accordingly. The black swirl denotes the shift of the ‘A-site’ adenosine to its new L-site position in Sa Hfq and the approximate rotation that is necessary for this movement is given in degrees. The same steric hindrances between S48 and F30 and the A-site adenosine are found in Bs Hfq thereby precluding A-site binding to that protein. (B) Ribbon diagram of the overlay of the crystal structures of Sa Hfq–A₄ (grey), Bs Hfq–(AG)₃A (blue), Ec Hfq–A₁₅ (magenta), and St Hfq–U₆ (orange) complexes. β strands 3 and 4 are labeled. An A-site-bound adenosine from the Ec Hfq–A₁₅ complex is shown as magenta sticks and labeled Ec A. Note the different twists of β strands 3 and 4 in Gram-positive and Gram-negative bacteria whereby the inward orientation of the β3 and β4 strands in Gram-positive bacteria obstructs an A-site adenosine from binding at this position. Sa Hfq residue S48 and corresponding Ec Hfq residue N48 are shown as blue and magenta sticks, respectively, to highlight their altered locations.