title: In silico analysis of family GH77 with focus on amylomaltases from borreliae and disproportionating enzymes DPE2 from plants and bacteria.
abstract: The CAZy glycoside hydrolase (GH) family GH77 is a monospecific family containing 4-α-glucanotransferases that if from prokaryotes are known as amylomaltases and if from plants including algae are known as disproportionating enzymes (DPE). The family GH77 is a member of the α-amylase clan GH-H. The main difference discriminating a GH77 4-α-glucanotransferase from the main GH13 α-amylase family members is the lack of domain C succeeding the catalytic (β/α)8-barrel. Of more than 2400 GH77 members, bacterial amylomaltases clearly dominate with more than 2300 sequences; the rest being approximately equally represented by Archaea and Eucarya. The main goal of the present study was to deliver a detailed bioinformatics study of family GH77 (416 collected sequences) focused on amylomaltases from borreliae (containing unique sequence substitutions in functionally important positions) and plant DPE2 representatives (possessing an insert of ~140 residues between catalytic nucleophile and proton donor). The in silico analysis reveals that within the genus of Borrelia a gradual evolutionary transition from typical bacterial Thermus-like amylomaltases may exist to family-GH77 amylomaltase versions that currently possess progressively mutated the most important and otherwise invariantly conserved positions. With regard to plant DPE2, a large group of bacterial amylomaltases represented by the amylomaltase from Escherichia coli with a longer N-terminus was identified as a probable intermediary connection between Thermus-like and DPE2-like (existing also among bacteria) family GH77 members. The presented results concerning both groups, i.e. amylomaltases from borreliae and plant DPE2 representatives (with their bacterial counterpart), may thus indicate the direction for future experimental studies.
authors.affiliation: Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia.
authors.forename: Andrea
authors.initials: A
authors.lastname: Kuchtová
authors.affiliation: Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia. Electronic address: Stefan.Janecek@savba.sk.
authors.forename: Štefan
authors.initials: Š
authors.lastname: Janeček
mesh_terms: D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000235:genetics; D001105:Archaea / Q000145:classification / Q000201:enzymology / Q000235:genetics; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D001898:Borrelia / Q000145:classification / Q000201:enzymology / Q000235:genetics; D030562:Databases, Protein; D004926:Escherichia coli / Q000145:classification / Q000201:enzymology / Q000235:genetics; D015870:Gene Expression; D006004:Glycogen Debranching Enzyme System / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D010944:Plants / Q000145:classification / Q000201:enzymology / Q000235:genetics; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D029681:Arabidopsis Proteins; D019843:Archaeal Proteins; D001426:Bacterial Proteins; C000592241:DPE2 protein, Arabidopsis; D006004:Glycogen Debranching Enzyme System; D010940:Plant Proteins; C020569:4 alpha-glucanotransferase
keywords: Amylomaltase; Bioinformatics analysis; Borreliae; Disproportionating enzyme; Evolutionary relatedness; Family GH77