Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme

C3 exoenzymes from bacterial pathogens ADP‐ribosylate and inactivate low‐molecular‐mass GTPases of the Rho subfamily. Ral, a Ras subfamily GTPase, binds the C3 exoenzymes from Clostridium botulinum and C. limosum with high affinity without being a substrate for ADP ribosylation. In the complex, the ADP‐ribosyltransferase activity of C3 is blocked, while binding of NAD and NAD‐glycohydrolase activity remain. Here we report the crystal structure of C3 from C. botulinum in a complex with GDP‐bound RalA at 1.8 Å resolution. C3 binds RalA with a helix–loop–helix motif that is adjacent to the active site. A quaternary complex with NAD suggests a mode for ADP‐ribosyltransferase inhibition. Interaction of C3 with RalA occurs at a unique interface formed by the switch‐II region, helix α3 and the P loop of the GTPase. C3‐binding stabilizes the GDP‐bound conformation of RalA and blocks nucleotide release. Our data indicate that C. botulinum exoenzyme C3 is a single‐domain toxin with bifunctional properties targeting Rho GTPases by ADP ribosylation and Ral by a guanine nucleotide dissociation inhibitor‐like effect, which blocks nucleotide exchange.