Biologia, Bratislava, 57/Suppl. 11: 29-41, 2002.
ISSN 0006-3088 (Biologia).
How many conserved sequence regions are there in the a-amylase family?
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: firstname.lastname@example.org
Received: May 7, 2002 / Accepted: May 31, 2002
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 wellconserved 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 b3®a3 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
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.