The sensor histidine kinase A (KinA) from Bacillus subtilis triggers a 
phosphorelay that activates sporulation. The antikinase KipI prevents 
sporulation by binding KinA and inhibiting the autophosphorylation reaction. 
Using neutron contrast variation, mutagenesis, and fluorescence data, we show 
that two KipI monomers bind via their C-domains at a conserved proline in the 
KinA dimerization and histidine-phosphotransfer (DHp) domain. Our crystal 
structure of the KipI C-domain reveals the binding motif has a distinctive 
hydrophobic groove formed by a five-stranded antiparallel beta-sheet; a 
characteristic of the cyclophilin family of proteins that bind prolines and 
often act as cis-trans peptidyl-prolyl isomerases. We propose that the DHp 
domain of KinA transmits conformational signals to regulate kinase activity via 
this proline-mediated interaction. Given that both KinA and KipI homologues are 
widespread in the bacterial kingdom, this mechanism has broad significance in 
bacterial signal transduction.