XC1028 from Xanthomonas campestris adopts a PilZ domain-like structure without a c-di-GMP switch

The crystal structure of XC1028 from Xanthomonas campestris has been determined to a resolution of 2.15 A using the multiple anomalous dispersion approach. It bears significant sequence identity and similarity values of 64.10% and 70.09%, respectively, with PA2960, a protein indispensable for type IV pilus-mediated twitching motility, after which the PilZ motif was first named. However, both XC1028 and PA2960 lack detectable c-di-GMP binding capability. Although XC1028 adopts a structure comprising a five-stranded beta-barrel core similar to other canonical PilZ domains with robust c-di-GMP binding ability, considerable differences are observed in the N-terminal motif; XC1028 assumes a compact five-stranded beta-barrel without an extra long N-terminal motif, whereas other canonical PilZ domains contain a long N-terminal sequence embedded with an essential "c-di-GMP switch" motif. In addition, a beta-strand (beta1) in the N-terminal motif, running in exactly opposite polarity to that of XC1028, is found inserted into the parallel beta3/beta1' strands, forming a completely antiparallel beta4 downward arrow beta3 upward arrow beta1 downward arrow beta1' upward arrow sheet in the canonical PilZ domains. Such dramatic structural differences at the N-terminus may account for the diminished c-di-GMP binding capability of XC1028, and suggest that interactions with additional proteins are necessary to bind c-di-GMP for type IV fimbriae assembly.