Delicate conformational changes of a protein in the CRP family lead to dramatic functional changes via binding of an...

CLP (c-AMP receptor protein like protein) from the plant pathogen Xanthomonas campestris (Xc) is a moderately strong c-di-GMP binder. After binding with c-di-GMP, XcCLP is dissociated from DNA, thus changing the expression profile of approximately 300 downstream genes, many of which are involved in the pathogenicity of Xc. To better understand the intricacies of this interesting regulation mechanism, a crystal structure of XcCLP has been determined to a resolution of 2.28 Å. This, in conjunction with an abundance of biochemical studies of mutants based on this structure, has illuminated a better understanding of c-di-GMP receptor. In this addendum, the following aspects of this unique protein shall be described from a more structural perspective: 1) Why c-di-GMP cannot bind to the c-NMP domain of XcCLP; 2) Why XcCLP can intrinsically bind to cognate DNA in the absence of any ligand; and 3) How c-di-GMP inhibits the DNA-binding capability of XcCLP, thus releasing XcCLP from DNA. Interestingly, the aforementioned questions are related by the subtle side-chain flipping of several key signature amino acids. In particular, through mutant studies and sequence alignments of proteins in the CRP family, four key signature amino acid residues have been identified that may allow one to distinguish whether a member in the CRP-FNR family is a c-AMP or a c-di-GMP responsive protein. In conclusion, a possible evolutionary pathway from EcCRP to XcCLP will be described.