α-amylase family: Molecular biology and evolution

Janeček, Štefan

doi:10.1016/s0079-6107(97)00015-1

Cited by 214 publications

(147 citation statements)

References 275 publications

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“…All known archaeal ␣-amylases with determined sequence were used. As far as the ␣-amylases from Eubacteria and Eucarya are concerned, respectively, they were chosen as representatives of previously identified evolutionary related groups (Raimbaud et al 1989;Janeček 1994Janeček , 1995Janeček , 1997Jespersen et al 1993;Janeček et al 1997). Thus the studied ␣-amylases represent a wide spectrum of taxonomically different species.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Janeček

Lévêque²,

Belarbi³

et al. 1999

J Mol Evol

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Abstract. The amino acid sequences of 22 ␣-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the evolutionary relationships between the archaeal ␣-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 ␤2, ␤3, ␤4, ␤5, ␤7, and ␤8 strand segments of the catalytic (␣/␤) 8 -barrel and a short conserved stretch in domain B protruding out of the barrel in the ␤3 → ␣3 loop, and (ii) the second one based on the alignment of the substantial continuous part of the (␣/␤) 8 -barrel involving the entire domain B (consensus length: 386 residues). With regard to archaeal ␣-amylases, both trees compared brought, in fact, the same results; i.e., all family 13 ␣-amylases from domain Archaea were clustered with barley pI isozymes, which represent all plant ␣-amylases. The enzymes from Bacillus licheniformis and Escherichia coli, representing liquefying and cytoplasmic ␣-amylases, respectively, seem to be the further closest relatives to archaeal ␣-amylases. This evolutionary relatedness clearly reflects the discussed similarities in the amino acid sequences of these ␣-amylases, especially in the bestconserved sequence regions. Since the results for ␣-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 ␣-amylase.

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Section: Methodsmentioning

confidence: 99%

“…Family 57 of ␣-amylases comprises a few amylolytic enzymes predominantly from hyperthermophiles (Bauer et al 1998). The present study deals with family 13 ␣-amylases (for a recent review, see Janeček 1997), which involves more than one hundred ␣-amylases belonging to all the three domains of life: Eucarya, Eubacteria, and Archaea.…”

Section: Introductionmentioning

confidence: 99%

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Janeček

Lévêque²,

Belarbi³

et al. 1999

J Mol Evol

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“…The tertiary structure of these enzymes is characterized by a (b/a) 8 barrel containing four highly conserved amino acid regions that form the active site (MacGregor et al, 2001), but the overall sequence similarity can be as low as 10 % and only a catalytic triad of amino acids is conserved invariantly (Machovic & Janecek, 2003). The shared (b/a) 8 barrel structure and catalytic mechanism within GH13 enzymes are believed to represent a common evolutionary origin (Kuriki & Imanaka, 1999;Janecek, 1997). The presence of the four conserved regions and a common secondary and tertiary structure allow construction of alignments and phylogenetic studies within the family.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal α-amylase enzymes

et al. 2007

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Currently known fungal a-amylases are well-characterized extracellular enzymes that are classified into glycoside hydrolase subfamily GH13_1. This study describes the identification, and phylogenetic and biochemical analysis of novel intracellular fungal a-amylases. The phylogenetic analysis shows that they cluster in the recently identified subfamily GH13_5 and display very low similarity to fungal a-amylases of family GH13_1. Homologues of these intracellular enzymes are present in the genome sequences of all filamentous fungi studied, including ascomycetes and basidiomycetes. One of the enzymes belonging to this new group, Amy1p from Histoplasma capsulatum, has recently been functionally linked to the formation of cell wall a-glucan. To study the biochemical characteristics of this novel cluster of a-amylases, we overexpressed and purified a homologue from Aspergillus niger, AmyD, and studied its activity product profile with starch and related substrates. AmyD has a relatively low hydrolysing activity on starch (2.2 U mg "1 ), producing mainly maltotriose. A possible function of these enzymes in relation to cell wall a-glucan synthesis is discussed. INTRODUCTIONa-Amylases are widely occurring enzymes which hydrolyse the a-(1,4)-glycosidic bonds in starch and glycogen, producing short maltooligosaccharides and maltose. Based on sequence similarity, most a-amylases (EC 3.2.1.1) are classified in glycoside hydrolase (GH) family 13, although some a-amylases originating from extremophilic organisms belong to family GH57 (Henrissat, 1991;Henrissat & Bairoch, 1996) (see also the CAZy website, http://www.cazy.org). Based on a phylogenetic analysis of 1691 different members of the GH13 family, the family has recently been divided into 35 subfamilies, all acting on aglycosidic bonds (Stam et al., 2006). Several of these subfamilies display a-amylase specificity, but many other enzyme reaction specificities are also represented. The tertiary structure of these enzymes is characterized by a (b/a) 8 barrel containing four highly conserved amino acid regions that form the active site (MacGregor et al., 2001), but the overall sequence similarity can be as low as 10 % and only a catalytic triad of amino acids is conserved invariantly (Machovic & Janecek, 2003). The shared (b/a) 8 barrel structure and catalytic mechanism within GH13 enzymes are believed to represent a common evolutionary origin (Kuriki & Imanaka, 1999;Janecek, 1997). The presence of the four conserved regions and a common secondary and tertiary structure allow construction of alignments and phylogenetic studies within the family. The phylogeny of a-amylases is generally in agreement with their origin, e.g. all fungal a-amylases are more related to each other than to the a-amylases originating from plants or animals. a-Amylases from bacteria, however, are scattered over several clusters, which group with animal, plant or fungal a-amylases, or form a separate branch (Janecek, 1994).Several a-amylases from yeasts and fungi have been studied previously (see e.g....

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“…Ca 2+ ions were found to play an important role in maintaining the correct conformation, thermostability and activity of α-amylases (Janecek 1997). Liu et al (2010) investigated the role of Ca 2+ -binding residues Asp231, Asp233 and Asp438 of B. amyloliquefaciens α-amylase on the enzyme properties by site-directed mutagenesis, and they observed no significant changes in Asp231 and Asp438 mutations, while Asp233 mutation resulted in a dramatic reduction of catalytic efficiency and thermostability at 60…”

Section: Discussionmentioning

confidence: 99%

Molecular cloning, overexpression and characterization of the raw-starch-digesting α-amylase of Bacillus amyloliquefaciens

et al. 2010

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Raw starch is the most abundant source of glucose in the world. Therefore, finding enzymes capable of digesting raw starch would find high industrial demand. The α-amylase gene of Bacillus amyloliquefaciens ATCC 23842 was amplified, cloned and overexpressed in Escherichia coli BL21 (DE3) cells. The recombinant enzyme was purified to apparent homogeneity using ion exchange and gel filtration chromatography. The raw-starch digestibility of the purified enzyme was characterized by studying the hydrolysis and adsorption rate on a variety of raw starches (potato, cassava, corn, wheat and rice). The raw-starch digestion was further confirmed by scanning electron microscopy studies, which revealed an effective rate of hydrolysis. The kinetic studies revealed a relatively low Km of 2.76 mg/mL, exhibiting high affinity towards the soluble starch as the most preferred substrate and the inhibition kinetic studies revealed a high Ki value (350 mM).

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α-amylase family: Molecular biology and evolution

Cited by 214 publications

References 275 publications

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal α-amylase enzymes

Molecular cloning, overexpression and characterization of the raw-starch-digesting α-amylase of Bacillus amyloliquefaciens

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