Carbohydrate-binding module tribes.
At present, 69 families of carbohydrate-binding modules (CBMs) have been isolated by statistically significant differences in the amino acid sequences (primary structures) of their members, with most members of different families showing 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, suggesting that they are descended from common protein ancestors. Members of the large majority of CBM families are β-sandwiches. This raises the question of whether members of different families are descended from distant common ancestors, and therefore are members of the same tribe. We have attacked this problem by attempting to computationally superimpose tertiary structure representatives of each of the 53 CBM families that have members with known tertiary structures. When successful, we have aligned locations of secondary structure elements and determined root mean square deviations and percentages of similarity between adjacent amino acid residues in structures from similar families. Further criteria leading to tribal membership are amino acid chain lengths and bound ligands. These considerations have led us to assign 27 families to nine tribes. Eight of the tribes have members with β-sandwich structures, while the ninth is composed of structures with β-trefoils.
Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011.
Caio C
CC
Carvalho
Ngoc N
NN
Phan
Yingfei
Y
Chen
Peter J
PJ
Reilly
D000595:Amino Acid Sequence; D001665:Binding Sites; D002241:Carbohydrates / Q000737:chemistry*; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D002241:Carbohydrates; D002352:Carrier Proteins
carbohydrate-binding module; protein family; protein tribe; secondary structure element; tertiary structure