Investigating diversity and similarity between CBM13 modules and ricin-B lectin domains using sequence similarity networks.

Autor: De Coninck T; Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, Ghent, 9000, Belgium.; Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium., Gippert GP; Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology & Biomedicine, Technical University of Denmark, Søltofts Plads 224, Kgs. Lyngby, 2800, Denmark., Henrissat B; Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology & Biomedicine, Technical University of Denmark, Søltofts Plads 224, Kgs. Lyngby, 2800, Denmark., Desmet T; Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium., Van Damme EJM; Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, Ghent, 9000, Belgium. elsjm.vandamme@ugent.be.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2024 Jun 27; Vol. 25 (1), pp. 643. Date of Electronic Publication: 2024 Jun 27.
DOI: 10.1186/s12864-024-10554-1
Abstrakt: Background: The CBM13 family comprises carbohydrate-binding modules that occur mainly in enzymes and in several ricin-B lectins. The ricin-B lectin domain resembles the CBM13 module to a large extent. Historically, ricin-B lectins and CBM13 proteins were considered completely distinct, despite their structural and functional similarities.
Results: In this data mining study, we investigate structural and functional similarities of these intertwined protein groups. Because of the high structural and functional similarities, and differences in nomenclature usage in several databases, confusion can arise. First, we demonstrate how public protein databases use different nomenclature systems to describe CBM13 modules and putative ricin-B lectin domains. We suggest the introduction of a novel CBM13 domain identifier, as well as the extension of CAZy cross-references in UniProt to guard the distinction between CAZy and non-CAZy entries in public databases. Since similar problems may occur with other lectin families and CBM families, we suggest the introduction of novel CBM InterPro domain identifiers to all existing CBM families. Second, we investigated phylogenetic, nomenclatural and structural similarities between putative ricin-B lectin domains and CBM13 modules, making use of sequence similarity networks. We concluded that the ricin-B/CBM13 superfamily may be larger than initially thought and that several putative ricin-B lectin domains may display CAZyme functionalities, although biochemical proof remains to be delivered.
Conclusions: Ricin-B lectin domains and CBM13 modules are associated groups of proteins whose database semantics are currently biased towards ricin-B lectins. Revision of the CAZy cross-reference in UniProt and introduction of a dedicated CBM13 domain identifier in InterPro may resolve this issue. In addition, our analyses show that several proteins with putative ricin-B lectin domains show very strong structural similarity to CBM13 modules. Therefore ricin-B lectin domains and CBM13 modules could be considered distant members of a larger ricin-B/CBM13 superfamily.
(© 2024. The Author(s).)
Databáze: MEDLINE
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