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Difference between revisions of "Polysaccharide Lyase Family 44"
Harry Brumer (talk | contribs) (Created page with "<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> {{UnderConstruct...") |
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== Substrate specificities == | == Substrate specificities == | ||
| − | + | Members of polysaccharide lyase family 44 have been shown to exhibit alginate lyase activity. The first member of this family is Aly44A, which originates from the bacterium ''Bacillus'' sp. FJAT-50079. (Genbank number WP_213137828.1). A total of 126 homologous sequences of Aly44A were identified by utilizing the BLASTp (with sequence coverage > 70% and identity > 40%) and CD-Hit tools. Meanwhile, four homologs of Aly44A exhibited the ability to degrade alginate (Zhou et al., 2024). | |
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Polysaccharide Lyase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)'' | Authors may get an idea of what to put in each field from ''Curator Approved'' [[Polysaccharide Lyase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)'' | ||
| Line 39: | Line 39: | ||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | The kinetic analysis showed that Aly44A exhibited higher conversion efficiency and a stronger affinity for polyM compared to polyG, indicating Aly44A was polyM-preferred. In contrast to bifunctional alginate lyases, which exhibited no preference for polyG or polyM, Aly44A showed superior potential in the preparation of alginate oligosaccharides consisting of M-blocks. It showed that Aly44A had a higher affinity and catalytic efficiency towards the polyM region of the longer-chain alginate (Zhou et al., 2024). | |
| + | |||
| + | == Action Pattern == | ||
| + | Based on the analysis of the action pattern, it showed that Aly44A was polyM-preferred. Aly44A was verified to exhibit a random endo-acting lyase activity to alginate. The final products of degradation were alginate oligosaccharides with DP 2-8, the main products of degradation were AOS with DP 2-4 as detected by UPSEC-MS (Zhou et al., 2024). | ||
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | No catalytic residues have been identified in this polysaccharide lyase family at present. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | The structure of Aly44A was predicted to be a parallel β-helix by AlphaFold2 (Zhou et al., 2024). | |
== Family Firsts == | == Family Firsts == | ||
| − | ;First stereochemistry determination: | + | ;First description of catalytic activity |
| − | ;First catalytic nucleophile identification: | + | The alginate lyase Aly44A was the first member of the family PL44 to be identified and characterized. |
| − | ;First general acid/base residue identification: | + | ;First stereochemistry determination: Not yet identified. |
| − | ;First 3-D structure: | + | ;First catalytic nucleophile identification: Not yet identified. |
| + | ;First general acid/base residue identification: Not yet identified. | ||
| + | ;First 3-D structure: Not yet identified. | ||
== References == | == References == | ||
<biblio> | <biblio> | ||
#Cantarel2009 pmid=18838391 | #Cantarel2009 pmid=18838391 | ||
| − | # | + | #Zhou, J., Li, J., Chen, G., Zheng, L., Mei, X., Xue, C., & Chang, Y. (2024). Discovery and characterization of a novel poly-mannuronate preferred alginate lyase: The first member of a new polysaccharide lyase family. Carbohydrate Polymers, 343, 122474.[https://doi.org/10.1042/BIO03004026 Download PDF version]. |
</biblio> | </biblio> | ||
[[Category:Polysaccharide Lyase Families|PL044]] | [[Category:Polysaccharide Lyase Families|PL044]] | ||
Revision as of 00:47, 13 October 2024
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
| Polysaccharide Lyase Family PL44 | |
| 3D Structure | |
| Mechanism | |
| Charge neutraliser | |
| Active site residues | |
| CAZy DB link | |
| https://www.cazy.org/PL44.html | |
Substrate specificities
Members of polysaccharide lyase family 44 have been shown to exhibit alginate lyase activity. The first member of this family is Aly44A, which originates from the bacterium Bacillus sp. FJAT-50079. (Genbank number WP_213137828.1). A total of 126 homologous sequences of Aly44A were identified by utilizing the BLASTp (with sequence coverage > 70% and identity > 40%) and CD-Hit tools. Meanwhile, four homologs of Aly44A exhibited the ability to degrade alginate (Zhou et al., 2024).
Authors may get an idea of what to put in each field from Curator Approved Polysaccharide Lyase Families. (TIP: Right click with your mouse and open this link in a new browser window...)
In the meantime, please see these references for an essential introduction to the CAZy classification system: [1, 2].
Kinetics and Mechanism
The kinetic analysis showed that Aly44A exhibited higher conversion efficiency and a stronger affinity for polyM compared to polyG, indicating Aly44A was polyM-preferred. In contrast to bifunctional alginate lyases, which exhibited no preference for polyG or polyM, Aly44A showed superior potential in the preparation of alginate oligosaccharides consisting of M-blocks. It showed that Aly44A had a higher affinity and catalytic efficiency towards the polyM region of the longer-chain alginate (Zhou et al., 2024).
Action Pattern
Based on the analysis of the action pattern, it showed that Aly44A was polyM-preferred. Aly44A was verified to exhibit a random endo-acting lyase activity to alginate. The final products of degradation were alginate oligosaccharides with DP 2-8, the main products of degradation were AOS with DP 2-4 as detected by UPSEC-MS (Zhou et al., 2024).
Catalytic Residues
No catalytic residues have been identified in this polysaccharide lyase family at present.
Three-dimensional structures
The structure of Aly44A was predicted to be a parallel β-helix by AlphaFold2 (Zhou et al., 2024).
Family Firsts
- First description of catalytic activity
The alginate lyase Aly44A was the first member of the family PL44 to be identified and characterized.
- First stereochemistry determination
- Not yet identified.
- First catalytic nucleophile identification
- Not yet identified.
- First general acid/base residue identification
- Not yet identified.
- First 3-D structure
- Not yet identified.
References
- Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |
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, J., Li, J., Chen, G., Zheng, L., Mei, X., Xue, C., & Chang, Y. (2024). Discovery and characterization of a novel poly-mannuronate preferred alginate lyase: The first member of a new polysaccharide lyase family. Carbohydrate Polymers, 343, 122474.Download PDF version.