ComAC and Spo0F bind to different Rap protein surfaces.
(A) Side view of the RapF-ComAC complex. (B) Side view of the RapH-Spo0F complex (3Q15) . This view was obtained by aligning RapH of the RapH-Spo0F complex with RapF of the RapF-ComAC complex as oriented in panel A and as described in (C). Dashed lines denote the RapH disordered region as described below. A comparison of panels A and B shows that ComAC and Spo0F bind to opposite faces of the RapF and RapH 3-helix bundles, respectively, and that Spo0F also interacts with the RapH TPR domain. (C) Side view of RapF of the RapF-ComAC structure aligned with RapH of the RapH-Spo0F structure. The RapF and RapH Cα backbone atoms aligned with a root mean-square deviation of 1.61 Å. We previously observed insufficient electron density corresponding to RapH residues 69–76, and they were not included in the RapH-Spo0F model . These residues correspond to the C-terminus of RapF helix α3 and a portion of the RapF linker region including the 310 helix. This region appears to be ordered in the RapF structure resulting from extensive interactions with ComA. Structural alignment of RapF of the RapF-ComAC structure with RapH of the RapH-Spo0F structure also revealed conformational differences in the regions surrounding the RapF and RapH α2–α3 loops. This area contains residues particularly important for Rap phosphatase activity, including a catalytic residue that inserts into the Spo0F active site. Thus, the conformational differences between RapF and RapH near the α2–α3 loop likely result from Spo0F binding to RapH.