Polysaccharide Lyase Family 44 - Revision history

Yaoguang Chang at 00:52, 26 October 2024

2024-10-26T00:52:04Z

Harry Brumer: added citation tags in text

2024-10-25T15:43:36Z

added citation tags in text

Jinhang Zhou at 07:27, 16 October 2024

2024-10-16T07:27:35Z

Jinhang Zhou at 07:27, 16 October 2024

2024-10-16T07:27:03Z

Jinhang Zhou at 07:25, 16 October 2024

2024-10-16T07:25:27Z

Jinhang Zhou at 07:22, 16 October 2024

2024-10-16T07:22:10Z

Jinhang Zhou at 08:47, 13 October 2024

2024-10-13T08:47:52Z

Harry Brumer: Created page with " {{UnderConstruct..."

2024-10-01T22:29:20Z

Created page with " {{UnderConstruct..."

New page

{{UnderConstruction}}
* [[Author]]: [[User:Jinhang Zhou|Jinhang Zhou]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL44'''
|-
|'''3D Structure'''
|
|-
|'''Mechanism'''
|
|-
|'''Charge neutraliser'''
|
|-
|'''Active site residues'''
|
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL44.html
|}
</div>


== Substrate specificities ==
Content is to be added here.

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: <cite>DaviesSinnott2008 Cantarel2009</cite>.

== Kinetics and Mechanism ==
Content is to be added here.

== Catalytic Residues ==
Content is to be added here.

== Three-dimensional structures ==
Content is to be added here.

== Family Firsts ==
;First stereochemistry determination: Content is to be added here.
;First catalytic nucleophile identification: Content is to be added here.
;First general acid/base residue identification: Content is to be added here.
;First 3-D structure: Content is to be added here.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026 Download PDF version].
</biblio>

[[Category:Polysaccharide Lyase Families|PL044]]

@@ Line 32: / Line 32: @@
 == 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).
+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>.
 == 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).
+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 ==
-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).
+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 ==
@@ Line 46: / Line 44: @@
 == Three-dimensional structures ==
-The structure of Aly44A was predicted to be a parallel β-helix by AlphaFold2 (Zhou et al., 2024).
+The structure of Aly44A was predicted to be a parallel β-helix by AlphaFold2 <cite>Zhou2024</cite>.
 == Family Firsts ==

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Jinhang Zhou|Jinhang Zhou]]
 * [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]

@@ Line 59: / Line 59: @@
 <biblio>
 #Zhou2024 pmid=39174099
 </biblio>
 [[Category:Polysaccharide Lyase Families|PL044]]

@@ Line 58: / Line 58: @@
 == References ==
 <biblio>
-#Zhou2024, PMID39174099
+#Zhou2024, PMID=39174099
 #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/10.1016/j.carbpol.2024.122474 Download PDF version].
 </biblio>
 [[Category:Polysaccharide Lyase Families|PL044]]

@@ Line 12: / Line 12: @@
 |-
 |'''3D Structure'''
+|parallel β-helix (AlphaFold)
 |-
 |'''Mechanism'''
+|poly-mannuronate preferred
 |-
 |'''Charge neutraliser'''
+|not known
 |-
 |'''Active site residues'''
+|not known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
@@ Line 34: / Line 34: @@
 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).
 == Kinetics and Mechanism ==
@@ Line 60: / Line 58: @@
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Zhou2024, PMID39174099
-#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].
+#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/10.1016/j.carbpol.2024.122474 Download PDF version].
 </biblio>
 [[Category:Polysaccharide Lyase Families|PL044]]

@@ Line 32: / Line 32: @@
 == Substrate specificities ==
-Content is to be added here.
+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...)''
@@ Line 39: / Line 39: @@
 == Kinetics and Mechanism ==
-Content is to be added here.
+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).
 == Catalytic Residues ==
-Content is to be added here.
+No catalytic residues have been identified in this polysaccharide lyase family at present.
 == Three-dimensional structures ==
-Content is to be added here.
+The structure of Aly44A was predicted to be a parallel β-helix by AlphaFold2 (Zhou et al., 2024).
 == Family Firsts ==
-;First stereochemistry determination: Content is to be added here.
+;First description of catalytic activity
-;First catalytic nucleophile identification: Content is to be added here.
+The alginate lyase Aly44A was the first member of the family PL44 to be identified and characterized.
-;First general acid/base residue identification: Content is to be added here.
+;First stereochemistry determination: Not yet identified.
-;First 3-D structure: Content is to be added here.
+;First catalytic nucleophile identification: Not yet identified.
 == References ==
 <biblio>
 #Cantarel2009 pmid=18838391
-#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026 Download PDF version].
+#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>
 [[Category:Polysaccharide Lyase Families|PL044]]