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In silico analysis of the α-amylase family GH57: eventual subfamilies reflecting enzyme specificities.

作者信息

Martinovičová Mária, Janeček Štefan

机构信息

1Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, 91701 Slovakia.

2Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, 84551 Slovakia.

出版信息

3 Biotech. 2018 Jul;8(7):307. doi: 10.1007/s13205-018-1325-9. Epub 2018 Jul 9.


DOI:10.1007/s13205-018-1325-9
PMID:29998051
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6037648/
Abstract

Glycoside hydrolases (GHs) have been classified in the CAZy database into 153 GH families. Currently, there might be four α-amylase families: the main family GH13, the family GH57 with related GH119 and, eventually, also GH126. The family GH57 was established in 1996 as the second and smaller α-amylase family. In addition to α-amylase, it contains 4-α-glucanotransferase, α-glucan branching enzyme, amylopullulanase, dual-specificity amylopullulanase-cyclomaltodextrinase, non-specified amylase, maltogenic amylase and α-galactosidase. The family GH57 enzymes employ the retaining reaction mechanism, share five typical conserved sequence regions and possess catalytic (β/α)-barrel succeeded by a four-helix bundle with the catalytic machinery consisting of catalytic nucleophile and proton donor (glutamic acid and aspartic acid at strands β4 and β7, respectively). The present bioinformatics study delivers a detailed sequence comparison of 1602 family GH57 sequences with the aim to highlight the uniqueness of each enzyme's specificity and all eventual protein groups. This was achieved by creating the evolutionary tree focused on both the enzyme specificities and taxonomical origin. The substantial increase of numbers of sequences from recent comparisons done more than 5 years ago has allowed to refine the details of the sequence logos for the individual enzyme specificities. The study identifies a new evolutionary distinct group of α-galactosidase-related enzymes with until-now-undefined enzyme specificity but positioned on the evolutionary tree on a branch adjacent to α-galactosidases. The specificity of α-galactosidase is, moreover, the only one of the entire family GH57 for which there is no structural support for the proposal of the proton donor based on sequence analysis. The analysis also suggests a few so-called "like" protein groups related to some family GH57 enzyme specificities but lacking one or both catalytic residues.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/188c/6037648/d66bc7897e09/13205_2018_1325_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/188c/6037648/d9261b05b7a7/13205_2018_1325_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/188c/6037648/3a3ec63df858/13205_2018_1325_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/188c/6037648/d66bc7897e09/13205_2018_1325_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/188c/6037648/d9261b05b7a7/13205_2018_1325_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/188c/6037648/3a3ec63df858/13205_2018_1325_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/188c/6037648/d66bc7897e09/13205_2018_1325_Fig3_HTML.jpg

相似文献

[1]
In silico analysis of the α-amylase family GH57: eventual subfamilies reflecting enzyme specificities.

3 Biotech. 2018-7

[2]
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[3]
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[4]
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[5]
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[6]
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[7]
In silico identification of catalytic residues and domain fold of the family GH119 sharing the catalytic machinery with the α-amylase family GH57.

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[8]
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[9]
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[10]
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[4]
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[5]
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[6]
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[7]
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Sci Rep. 2021-5-3

[8]
Aspects and Recent Trends in Microbial α-Amylase: a Review.

Appl Biochem Biotechnol. 2021-8

[9]
Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains.

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[10]
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本文引用的文献

[1]
GH57 amylopullulanase from Desulfurococcus amylolyticus JCM 9188 can make highly branched cyclodextrin via its transglycosylation activity.

Enzyme Microb Technol. 2018-3-16

[2]
Sequence analysis and biochemical properties of an acidophilic and hyperthermophilic amylopullulanase from Thermofilum pendens.

Int J Biol Macromol. 2018-3-16

[3]
GenBank.

Nucleic Acids Res. 2018-1-4

[4]
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.

Evolution. 1985-7

[5]
Structural basis for the transglycosylase activity of a GH57-type glycogen branching enzyme from Pyrococcus horikoshii.

Biochem Biophys Res Commun. 2017-3-18

[6]
UniProt: the universal protein knowledgebase.

Nucleic Acids Res. 2017-1-4

[7]
Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family.

Cell Mol Life Sci. 2016-7

[8]
Membrane-bound amylopullulanase is essential for starch metabolism of Sulfolobus acidocaldarius DSM639.

Extremophiles. 2015-9

[9]
A GH57 4-α-glucanotransferase of hyperthermophilic origin with potential for alkyl glycoside production.

Appl Microbiol Biotechnol. 2015-2-19

[10]
Preparation of linear maltodextrins using a hyperthermophilic amylopullulanase with cyclodextrin- and starch-hydrolysing activities.

Carbohydr Polym. 2014-11-28

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