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

3 Biotech
Mária Martinovičová, S Janecek

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)7-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 ...Continue Reading

References

Nov 15, 1991·The Biochemical Journal·H M JespersenB Svensson
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jul 1, 1987·Molecular Biology and Evolution·N Saitou, M Nei
Jun 1, 1996·The Biochemical Journal·B Henrissat, A Bairoch
Jan 1, 1997·Progress in Biophysics and Molecular Biology·S Janecek
Sep 28, 2000·Current Opinion in Chemical Biology·C S Rye, S G Withers
Mar 21, 2001·Biochimica Et Biophysica Acta·E A MacGregorB Svensson
Feb 14, 2002·Journal of Biotechnology·Marc J E C van der MaarelL Dijkhuizen
Mar 6, 2003·The Journal of Biological Chemistry·Hiromi ImamuraHiroshi Matsuzawa
May 26, 2004·Biochemical and Biophysical Research Communications·Hiromi ImamuraTakayoshi Wakagi
May 27, 2004·Proteins·Maxim ShatskyHaim J Wolfson
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Nov 27, 2004·Bioscience, Biotechnology, and Biochemistry·Masahiro NakajimaTakayoshi Wakagi
Oct 20, 2005·Journal of Bioscience and Bioengineering·T Kuriki, T Imanaka
Mar 3, 2006·Acta Crystallographica. Section D, Biological Crystallography·Achim DickmannsRalf Ficner
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Oct 8, 2008·Nucleic Acids Research·Brandi L CantarelBernard Henrissat
Feb 28, 2009·Nature Protocols·Lawrence A Kelley, Michael J E Sternberg
Jul 17, 2010·Applied Biochemistry and Biotechnology·Phillip BrummDavid Mead
Apr 8, 2011·Nucleic Acids Research·Ivica Letunic, Peer Bork
Sep 10, 2011·Proteins·Elizabeth Ficko-BleanAlisdair B Boraston
Apr 25, 2012·Extremophiles : Life Under Extreme Conditions·Karol Blesák, Stefan Janeček
Jun 29, 2013·Cellular and Molecular Life Sciences : CMLS·Štefan JanečekE Ann MacGregor
Jul 26, 2013·Applied Microbiology and Biotechnology·Jong-Hyun JungCheon-Seok Park

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Citations

Jun 14, 2019·Applied Microbiology and Biotechnology·Xuewen ZhangMarc J E C van der Maarel
Nov 18, 2019·Extremophiles : Life Under Extreme Conditions·Štefan Janeček, Barbora Zámocká
Sep 20, 2019·Biotechnology Advances·Štefan JanečekBirte Svensson
Mar 15, 2021·Applied Biochemistry and Biotechnology·Jai Shankar PaulShailesh Kumar Jadhav
Jul 8, 2020·Carbohydrate Research·Lenka Kerényiová, Štefan Janeček
Jun 21, 2021·Biotechnology Advances·Wei XiaJing Wu
Aug 7, 2019·Journal of Agricultural and Food Chemistry·Bo PangZhemin Zhou

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Software Mentioned

MultiProt
iTOL
Phyre
WebLabViewerLite
Clustal
BLAST

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