At present, 66 families of carbohydrate-binding modules (CBMs) have been isolated by statistically significant differences in the amino acid sequences (primary structures) of their members, and in fact most members of different families show little if any homology. On the other hand, members of the same family have primary and tertiary (three-dimensional) structures that can be computationally aligned, yielding at least some degree of homology, and suggesting that they are descended from common protein ancestors. Almost universally, CBMs are composed of �-strands, with an almost total absence of a-helices. In addition, members of the large majority of CBM families are �-sandwiches, also known as �-jelly rolls. This raises the question of whether members of different families are descended from distant common ancestors, and therefore are members of the same clan, even though their primary structures may no longer retain any similarity. We have attacked this problem by attempting to computationally superimpose tertiary structure representatives of each of the 51 CBM families that have members with known tertiary structures, using MultiProt. In cases where visual observation has suggested that tertiary structures of different families are very similar, we have determined root mean square deviations (RMSD) and percentages of similarity between adjacent amino acid residues in the two structures. Further criteria beyond low RMSDs and high similarity percentages leading to clan membership are similarities in locations of secondary structure elements, amino acid chain lengths, and bound ligands. These considerations have led us to assign 31 families to seven clans, with two to seven families in each clan. Five of the clans have members with �-sandwiches having six to ten �-strands, while a sixth is composed of structures with �-trefoils, and a seventh has very short chains with only two to four short �-strands.

Carbohydrate binding module clans

248th National Meeting (2014)

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