Several important bacterial processes are regulated by cyclic di-GMP (c-di-GMP) signalling. Wang et al. report a novel mode of c-di-GMP binding by the MshE amino-terminal (MshEN) domain, which has recently been shown to specifically and potently bind to c-di-GMP. A 1.37 Å-resolution structure of a Vibrio cholerae MshEN domain showed that c-di-GMP binds to two motifs of 24 conserved residues that do not share homology with canonical c-di-GMP-binding motifs; the functional importance of conserved residues was confirmed by mutant phenotypes that were defective in pilin production and biofilm formation. Furthermore, kinetic experiments demonstrated a binding affinity for c-di-GMP that was ten-fold stronger than the PilZ c-di-GMP-binding domain. Finally, the authors found that MshEN is widely distributed in bacteria, which suggests that it is an ancient regulator and may explain the basis for c-di-GMP signalling in bacteria that lack known c-di-GMP receptors.