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Evolution of β‐amylase: Patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms
Author(s) -
Pujadas Gerard,
Ramírez Flora M.,
Valero Ricard,
Palau Jaume
Publication year - 1996
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199608)25:4<456::aid-prot6>3.0.co;2-b
Subject(s) - amylase , biology , subfamily , evolutionary biology , molecular evolution , phylogenetic tree , phylogenetics , computational biology , genetics , gene , enzyme , biochemistry
Soybean and sweet potato β‐amylases are structured as α/β barrels and the same kind of folding may account for all known β‐amylases. We provide a comprehensive analysis of both protein and DNA (coding region) sequences of β‐amylases. The aim of the study is to contribute to the knowledge of the evolutionary molecular relationships among all known β‐amylases. Our approach combines the identification of the putative eightfold structural core formed by β‐strands with a complete multi‐alignment analysis of all known sequences. Comparing putative β‐amylase (α/β) 8 cores from plants and microorganisms, two differentiated versions of residues at the packing sites, and a unique set of eight identical residues at the C‐terminal catalytical site are observed, indicating early evolutionary divergence and absence of localized three‐dimensional evolution, respectively. A new analytical approach has been developed in order to work out conserved motifs for β‐amylases, mostly related with the enzyme activity. This approach appears useful as a new routine to find sets of motifs (each set being known as a fingerprint) in protein families. We demonstrate that the evolutionary mechanism for β‐amylases is a combination of parsimonious divergence at three distinguishable rates in relation to the functional signatures, the barrel scaffold, and α‐helix‐containing loops. © 1996 Wiley‐Liss, Inc.