The structural basis of cyclic diguanylate signal transduction by PilZ domains

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Abstract
The second messenger cyclic diguanylate (c‐di‐GMP) controls the transition between motile and sessile growth in eubacteria, but little is known about the proteins that sense its concentration. Bioinformatics analyses suggested that PilZ domains bind c‐di‐GMP and allosterically modulate effector pathways. We have determined a 1.9 Å crystal structure of c‐di‐GMP bound to VCA0042/PlzD, a PilZ domain‐containing protein from Vibrio cholerae . Either this protein or another specific PilZ domain‐containing protein is required for V. cholerae to efficiently infect mice. VCA0042/PlzD comprises a C‐terminal PilZ domain plus an N‐terminal domain with a similar β‐barrel fold. C‐di‐GMP contacts seven of the nine strongly conserved residues in the PilZ domain, including three in a seven‐residue long N‐terminal loop that undergoes a conformational switch as it wraps around c‐di‐GMP. This switch brings the PilZ domain into close apposition with the N‐terminal domain, forming a new allosteric interaction surface that spans these domains and the c‐di‐GMP at their interface. The very small size of the N‐terminal conformational switch is likely to explain the facile evolutionary diversification of the PilZ domain.