Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all β-trefoil proteins

Determination of the structures of fibroblast growth factors and interleukin-1s has previously revealed that they both adopt a β-trefoil fold, similar to those found in Kunitz soybean trypsin inhibitors, ricin-like toxins, plant agglutinins and hisactophilin. These families possess distinct functions and occur in different subcellular localisations, and they appear to lack significant similarities in their sequences, ligands and modes of ligand binding. We have analysed the significance of sequence identities observed after structure alignment and provide statistical evidence that these β-trefoil proteins are all homologues, having arisen from a common ancestor. In addition, we have explored the sequence space of all β-trefoil proteins and have determined that the actin-binding proteins fascins, and other proteins of unknown function, are β-trefoil family homologues. Unlike other β-trefoil proteins, the triplicated repeats in each of the four β-trefoil domains of fascins are significantly similar in sequence. This hints at how the β-trefoil fold arose from the duplication of an ancestral gene encoding a homotrimeric single-repeat protein. The combined analysis of structure and sequence databases for detecting significant similarities is suggested as a highly sensitive approach to determining the common ancestry of extremely divergent homologues.