Crystal structure of the putative peptide‐binding protein AppA from Clostridium difficile

Peptides play an important signalling role in Bacillus subtilis, where their uptake by one of two ABC‐type oligopeptide transporters, Opp and App, is required for efficient sporulation. Homologues of these transporters in Clostridium difficile have been characterized, but their role, and hence that of peptides, in regulating sporulation in this organism is less clear. Here, the oligopeptide‐binding receptor proteins for these transporters, CdAppA and CdOppA, have been purified and partially characterized, and the crystal structure of CdAppA has been determined in an open unliganded form. Peptide binding to either protein could not be observed in Thermofluor assays with a set of ten peptides of varying lengths and compositions. Re‐examination of the protein sequences together with structure comparisons prompts the proposal that CdAppA is not a versatile peptide‐binding protein but instead may bind a restricted set of peptides. Meanwhile, CdOppA is likely to be the receptor protein for a nickel‐uptake system. CdOppA and CdAppA are putative extracellular peptide‐binding proteins serving cognate ABC transporters in Clostridium difficile. Using purified proteins, no evidence was found for (i) peptide binding to either protein in Thermofluor experiments or (ii) the presence of peptides in the crystal structure of CdAppA. Further sequence analysis suggests that CdOppA is a nickel‐transporter protein and that CdAppA may be involved in the transport of a restricted set of peptides.