Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

The rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-l-arabinofuranosidase, β-d-xylosidase, α-l-arabinanase, and β-d-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin poly...

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Bibliographic Details
Published in:Applied and environmental microbiology 2016-03, Vol.82 (6), p.1686-1692
Main Authors: Mewis, Keith, Lenfant, Nicolas, Lombard, Vincent, Henrissat, Bernard
Format: Article
Language:English
Subjects:
Biochemistry, Molecular Biology
Cellulose
Deoxyribonucleic acid
DNA
Enzymology and Protein Engineering
Glycoside Hydrolases - chemistry
Glycoside Hydrolases - classification
Glycoside Hydrolases - genetics
Glycoside Hydrolases - metabolism
Hydrolysis
Life Sciences
Pectin
Pectins - metabolism
Polymers
Polysaccharides - metabolism
Protein Domains
Proteins
Quantitative Methods
Structural Biology
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Summary:The rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-l-arabinofuranosidase, β-d-xylosidase, α-l-arabinanase, and β-d-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides.
ISSN:0099-2240
1098-5336
DOI:10.1128/AEM.03453-15