title: Evolution of beta-amylase: patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms.
abstract: Soybean and sweet potato beta-amylases are structured as alpha/beta barrels and the same kind of folding may account for all known beta-amylases. We provide a comprehensive analysis of both protein and DNA (coding region) sequences of beta-amylases. The aim of the study is to contribute to the knowledge of the evolutionary molecular relationships among all known beta-amylases. Our approach combines the identification of the putative eightfold structural core formed by beta-strands with a complete multi-alignment analysis of all known sequences. Comparing putative beta-amylase (alpha/beta)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 beta-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 beta-amylases is a combination of parsimonious divergence at three distinguishable rates in relation to the functional signatures, the barrel scaffold, and alpha-helix-containing loops.
authors.affiliation: Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Catalonia, Spain.
authors.forename: G
authors.initials: G
authors.lastname: Pujadas
authors.forename: F M
authors.initials: FM
authors.lastname: Ramírez
authors.forename: R
authors.initials: R
authors.lastname: Valero
authors.forename: J
authors.initials: J
authors.lastname: Palau
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D001614:beta-Amylase / Q000737:chemistry / Q000235:genetics*
chemical_list: D004247:DNA; D001614:beta-Amylase