Structural similarities and evolutionary relationships in chloride-dependent alpha-amylases.
The alpha-amylase sequences contained in databanks were screened for the presence of amino acid residues Arg195, Asn298 and Arg/Lys337 forming the chloride-binding site of several specialized alpha-amylases allosterically activated by this anion. This search provides 38 alpha-amylases potentially binding a chloride ion. All belong to animals, including mammals, birds, insects, acari, nematodes, molluscs, crustaceans and are also found in three extremophilic Gram-negative bacteria. An evolutionary distance tree based on complete amino acid sequences was constructed, revealing four distinct clusters of species. On the basis of multiple sequence alignment and homology modeling, invariable structural elements were defined, corresponding to the active site, the substrate binding site, the accessory binding sites, the Ca(2+) and Cl(-) binding sites, a protease-like catalytic triad and disulfide bonds. The sequence variations within functional elements allowed engineering strategies to be proposed, aimed at identifying and modifying the specificity, activity and stability of chloride-dependent alpha-amylases.
Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000, Liège, Belgium. sdamico@ulg.ac.be
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D'Amico
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Gerday
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Feller
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D002384:Catalysis; D002712:Chlorides / Q000378:metabolism; D004220:Disulfides; D019143:Evolution, Molecular; D006801:Humans; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011485:Protein Binding; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D000516:alpha-Amylases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
D002712:Chlorides; D004220:Disulfides; D000516:alpha-Amylases; D012697:Serine Endopeptidases; D002118:Calcium