Alpha plus beta folds revisited: some favoured motifs

Abstract

Background: By performing extensive pairwise structural comparisons, we recently identified a set of unique folds from the Brookhaven protein structure data bank. This analysis revealed considerable similarities between a large subgroup of the alpha+beta folds, which led us to re-examine the types of folds occurring in this class and the nature of the relationships between them.

Results: Two major alpha+beta fold groups can be distinguished. In the first, described as alpha-beta sandwiches because alpha-helices and beta-strands occupy separate and distinct layers, a split beta alpha beta motif recurs frequently. The other group, alpha-beta rolls, contains fewer helices and is more diverse. In these, the beta-sheet has folded or rolled over, providing a cradle for the alpha-helix. A beta beta beta alpha-meander motif is found throughout the alpha+beta class.

Conclusion: Although many alpha-beta sandwiches have very similar folds, few share common functions and the active sites are distributed over the whole surface of the fold. The ability of the alpha-beta sandwich to accommodate a range of functions suggests that it is a stable fold and one that is able to adapt a number of sites to satisfy different functional requirements. In contrast, amongst the alpha-beta rolls, folds having the same roll type often have common functions.