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Difference between revisions of "Polysaccharide Lyase Family 44"
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<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | ||
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* [[Author]]: [[User:Jinhang Zhou|Jinhang Zhou]] | * [[Author]]: [[User:Jinhang Zhou|Jinhang Zhou]] | ||
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]] | * [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]] | ||
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|- | |- | ||
|'''3D Structure''' | |'''3D Structure''' | ||
| − | | | + | |parallel β-helix (AlphaFold) |
|- | |- | ||
|'''Mechanism''' | |'''Mechanism''' | ||
| − | | | + | |poly-mannuronate preferred |
|- | |- | ||
|'''Charge neutraliser''' | |'''Charge neutraliser''' | ||
| − | | | + | |not known |
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |not known |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
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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 | + | 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 <cite>Zhou2024</cite>. |
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== 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 | + | 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 <cite>Zhou2024</cite>. |
== Action Pattern == | == 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 | + | 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 <cite>Zhou2024</cite>. |
== Catalytic Residues == | == Catalytic Residues == | ||
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== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | The structure of Aly44A was predicted to be a parallel β-helix by AlphaFold2 | + | The structure of Aly44A was predicted to be a parallel β-helix by AlphaFold2 <cite>Zhou2024</cite>. |
== Family Firsts == | == Family Firsts == | ||
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== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Zhou2024 pmid=39174099 |
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</biblio> | </biblio> | ||
[[Category:Polysaccharide Lyase Families|PL044]] | [[Category:Polysaccharide Lyase Families|PL044]] | ||
Latest revision as of 16:52, 25 October 2024
This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.
| Polysaccharide Lyase Family PL44 | |
| 3D Structure | parallel β-helix (AlphaFold) |
| Mechanism | poly-mannuronate preferred |
| Charge neutraliser | not known |
| Active site residues | not known |
| 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 [1].
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 [1].
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 [1].
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 [1].
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.