The (betaalpha) (8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships
Nagano, N.; Porter, C.T.; Thornton, J.M.
Protein Engineering 14(11): 845-855
2001
ISSN/ISBN: 0269-2139 PMID: 11742103 Document Number: 534374
There are currently at least nine distinct glycosidase sequence families which are all known to adopt a TIM barrel fold (Henrissat,B. and Davies,G. (1997) Curr. Opin. Struct. Biol., 7, 637-644). To explore the relationships between these enzymes and their evolution, comprehensive sequence and structure comparisons were performed, generating four distinct clusters. The first cluster, S1, comprises the alpha-amylase related enzymes, all with the retention mechanism (axialfwdarwaxial). The second cluster, S2, included two functional subgroups, one composed of various kinds of glucosidases all with the retention mechanism (equatorialfwdarwequatorial) (the so-called 4/7 superfamily), and the other subgroup including the beta-amylases with the inversion mechanism (axialfwdarwequatorial). The third cluster, S3, with the retention mechanism (equatorialfwdarwequatorial), could be subdivided, based on the catalytic residues and mechanisms, into two functional subgroups: the chitinase group, catalysed by two acidic residues on the C-termini of beta-4 and beta-6, and the hevamine group, using two acidic residues on the C-termini of beta-4 for catalysis. The fourth cluster, S4, is composed of chitobiase with the retention mechanism (equatorialfwdarwequatorial). These clusters are compared with the sequence families derived by Henrissat and coworkers. PSI-BLAST profiles and multiple-alignments of tertiary structures suggest that S1 and S2 are distantly related, as are S3 and S4, which have N-acetylated substrates. This work highlights the difficulties of untangling distant evolutionary relationships in ubiquitous folds such as the TIM barrel.