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J Mol Evol. 1999 Apr;48(4):421-6.

Close evolutionary relatedness of alpha-amylases from Archaea and plants.

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Institute of Microbiology, Slovak Academy of Sciences, Stefánikova 3, SK-81434 Bratislava, Slovakia.


The amino acid sequences of 22 alpha-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the evolutionary relationships between the archaeal alpha-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary distance trees were constructed: (i) the first one based on the alignment of extracted best-conserved sequence regions (58 residues) comprising beta2, beta3, beta4, beta5, beta7, and beta8 strand segments of the catalytic (alpha/beta)8-barrel and a short conserved stretch in domain B protruding out of the barrel in the beta3 --> alpha3 loop, and (ii) the second one based on the alignment of the substantial continuous part of the (alpha/beta)8-barrel involving the entire domain B (consensus length: 386 residues). With regard to archaeal alpha-amylases, both trees compared brought, in fact, the same results; i.e., all family 13 alpha-amylases from domain Archaea were clustered with barley pI isozymes, which represent all plant alpha-amylases. The enzymes from Bacillus licheniformis and Escherichia coli, representing liquefying and cytoplasmic alpha-amylases, respectively, seem to be the further closest relatives to archaeal alpha-amylases. This evolutionary relatedness clearly reflects the discussed similarities in the amino acid sequences of these alpha-amylases, especially in the best-conserved sequence regions. Since the results for alpha-amylases belonging to all three domains (Eucarya, Eubacteria, Archaea) offered by both evolutionary trees are very similar, it is proposed that the investigated conserved sequence regions may indeed constitute the "sequence fingerprints" of a given alpha-amylase.

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