Biologia, Bratislava, 57/Suppl. 11: 29-41, 2002.

ISSN 0006-3088 (Biologia).

 

Review

How many conserved sequence regions are there in the a-amylase family?

 

Stefan Janecek*

Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, SK-84551 Bratislava, Slovakia; tel.: ++ 421 2 5930 7420, fax: ++ 421 2 5930 7416, e-mail: umikstef@savba.sk

* corresponding author

Received: May 7, 2002 / Accepted: May 31, 2002

 

Abstract

The a-amylase family, i.e. the clan GH-H of glycoside hydrolases, is the largest family of glycoside hydrolases, transferases and isomerases comprising nearly 30 different enzyme specificities. One of the most interesting features of this family is that its members contain a few very well-conserved sequence regions despite the overall low sequence similarity. It seems that only 4 amino acid residues may be totally invariantly conserved throughout the family (Arg204 plus the three catalytic residues: Asp206, Glu230 and Asp297; Taka-amylase A numbering). Four conserved sequence regions covering the strands b3, b4, b5, and b7 of the catalytic (b/a)8-barrel domain were identified and used for defining the a-amylase family. The present review is therefore focused on the three additional conserved sequence regions proposed after the basic characteristics of the family have been established. Two of these three regions cover roughly the strands b2 and b8 of the catalytic (b/a)8-barrel and one is located near the C-terminus of domain B (in the b3a3 connection of the catalytic (b/a)8-barrel). While the four original conserved sequence regions contain the catalytic and substrate-binding residues of the individual members of the family, the three conserved sequence regions later identified are shown to contain amino acid residues connected to a given enzyme specificity. The problems that may arise with correctly identifying the b5-strand catalytic glutamate, positioned in the conserved sequence region III, is are discussed and athe way that may lead to a correct solution is indicated. In conclusion, it is proposed that the a-amylase enzyme family should be characterised by as many conserved sequence regions as possible.

 

Key words: alpha-amylase family, conserved sequence regions, sequence similarities, specificity features, evolutionary relationships.