CAZypedia - User contributions [en-ca]

User:Yaoguang Chang

2024-10-18T03:32:39Z

Jinhang Zhou:

[[File:Yaoguang Chang.jpg|100px|right]]
Yaoguang Chang obtained his Ph.D. degree from the Ocean University of China and was a visiting scholar at the University of Massachusetts Amherst. At present, he is a professor at the College of Food Science and Engineering, Ocean University of China. His research interests involve the gene-mining and characterization of [[Carbohydrate-active enzymes|CAZymes]] and [[carbohydrate-binding modules]] from marine polysaccharides. By utilizing the enzymes and binding proteins as critical tools, novel identification, quantification, and modification methods of marine polysaccharides were established, which would consequently facilitate the development and application of promising functional polysaccharides from the ocean.
His research group discovered the first member of [[GH168]], [[GH174]], [[GH187]], [[PL44]], [[CBM92]], [[CBM99]],[[CBM101]] and [[CBM106]] families, and contributed to the studies related to members of the following families:

*[[GH16]]: κ-carrageenase Cgk16A <cite>Shen2018</cite>, βκ-carrageenase Cgbk16A_Wf <cite>Cao2021</cite>, β-porphyranase Por16A_Wf <cite>Zhang2019</cite>, and β-porphyranase Por16C_Wf <cite>Zhang2020</cite>
*[[GH29]]: fucosidase Alf1_Wf <cite>Dong2017</cite>
*[[GH82]]: ι-carrageenase Cgi82A <cite>Shen2017</cite>
*[[GH86]]: β-agarase Aga86A_Wa <cite>Cao2020 Zhang2023</cite>
*[[GH168]]: endo-1,3-fucanase Fun168A <cite>Shen2020</cite>
*[[GH174]]: endo-1,3-fucanase Fun174A <cite>Liu2023</cite>
*[[PL7]]: alginate lyase Aly7B_Wf <cite>Pei2019</cite>
*[[PL44]]: alginate lyase Aly44A <cite>Zhou2024</cite>
*[[CBM16]]: ABP_Wf (alginate-binding CBM) <cite>Mei2020</cite>
*[[CBM47]]: WfCBM47 (sulfated fucan-binding CBM) <cite>Mei2022a</cite>
*[[CBM70]]: SrCBM70 (hyaluronic acid-binding CBM) <cite>Mei2022b</cite>
*[[CBM92]]: Cgk16A-CBM92 (carrageenan-binding CBM) <cite>Mei2022c</cite>
*CBMnc: Fun174A-CBM (sulfated fucan-binding CBM) <cite>Mei2023</cite>
*[[CBM99]]: FvCBM99 (porphyran-binding CBM) <cite>Mei2023a</cite>
*[[CBM101]]: WfCBM101 (agarose-binding CBM) <cite>Mei2023b</cite>
*[[GH187]]: endo-1,3-fucanase Fun187A <cite>Shen2024</cite>
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>
Some of the above biotechnological tools have been successfully integrated with glycomics <cite>Chen2021 Chen2023</cite>, lateral flow immunoassay <cite>Mei2022b</cite>, and other techniques, and served in the structural and chemical investigation of marine polysaccharides. And some enzymes have been employed to produce low molecular weight polysaccharides and oligosaccharides with verified bioactivities <cite>Cheng2022 Li2021</cite>.

== References ==
<biblio>
#Shen2018 pmid=29355636
#Cao2021 pmid=34421852
#Zhang2019 pmid=31352784
#Zhang2020 pmid=32520542
#Dong2017 pmid=27576198
#Shen2017 pmid=28760444
#Cao2020 pmid=32578425
#Zhang2023 pmid=36746585
#Shen2020 pmid=32849348
#Liu2023 pmid=36746582
#Pei2019 pmid=30248453
#Mei2020 pmid=32747278
#Mei2022a pmid=34893209
#Mei2022b pmid=36395930
#Mei2022c pmid=35830544
#Mei2023 pmid=36924869
#Chen2021 pmid=34420739
#Chen2023 pmid=37059545
#Cheng2022 pmid=35667104
#Li2021 pmid=34415766
#Zhou2024 pmid=39174099
#Mei2023a pmid=37769778
#Mei2023b pmid=38010608
#Mei2024 pmid=39069041
</biblio>


[[Category:Contributors|Chang,Yaoguang]]

User:Yaoguang Chang

2024-10-18T03:19:02Z

Jinhang Zhou:

[[File:Yaoguang Chang.jpg|100px|right]]
Yaoguang Chang obtained his Ph.D. degree from the Ocean University of China and was a visiting scholar at the University of Massachusetts Amherst. At present, he is a professor at the College of Food Science and Engineering, Ocean University of China. His research interests involve the gene-mining and characterization of [[Carbohydrate-active enzymes|CAZymes]] and [[carbohydrate-binding modules]] from marine polysaccharides. By utilizing the enzymes and binding proteins as critical tools, novel identification, quantification, and modification methods of marine polysaccharides were established, which would consequently facilitate the development and application of promising functional polysaccharides from the ocean.
His research group discovered the first member of [[GH168]], [[GH174]], [[PL44]], [[CBM92]], [[CBM99]] and [[CBM101]] families, and contributed to the studies related to members of the following families:

*[[GH16]]: κ-carrageenase Cgk16A <cite>Shen2018</cite>, βκ-carrageenase Cgbk16A_Wf <cite>Cao2021</cite>, β-porphyranase Por16A_Wf <cite>Zhang2019</cite>, and β-porphyranase Por16C_Wf <cite>Zhang2020</cite>
*[[GH29]]: fucosidase Alf1_Wf <cite>Dong2017</cite>
*[[GH82]]: ι-carrageenase Cgi82A <cite>Shen2017</cite>
*[[GH86]]: β-agarase Aga86A_Wa <cite>Cao2020 Zhang2023</cite>
*[[GH168]]: endo-1,3-fucanase Fun168A <cite>Shen2020</cite>
*[[GH174]]: endo-1,3-fucanase Fun174A <cite>Liu2023</cite>
*[[PL7]]: alginate lyase Aly7B_Wf <cite>Pei2019</cite>
*[[PL44]]: alginate lyase Aly44A <cite>Zhou2024</cite>
*[[CBM16]]: ABP_Wf (alginate-binding CBM) <cite>Mei2020</cite>
*[[CBM47]]: WfCBM47 (sulfated fucan-binding CBM) <cite>Mei2022a</cite>
*[[CBM70]]: SrCBM70 (hyaluronic acid-binding CBM) <cite>Mei2022b</cite>
*[[CBM92]]: Cgk16A-CBM92 (carrageenan-binding CBM) <cite>Mei2022c</cite>
*CBMnc: Fun174A-CBM (sulfated fucan-binding CBM) <cite>Mei2023</cite>
*[[CBM99]]: FvCBM99 (porphyran-binding CBM) <cite>Mei2023a</cite>
*[[CBM101]]: WfCBM101 (agarose-binding CBM) <cite>Mei2023b</cite>
*[[GH187]]: endo-1,3-fucanase Fun187A <cite>Shen2024</cite>
GH187: 87endo-1,3-fucanase Fun187A
Some of the above biotechnological tools have been successfully integrated with glycomics <cite>Chen2021 Chen2023</cite>, lateral flow immunoassay <cite>Mei2022b</cite>, and other techniques, and served in the structural and chemical investigation of marine polysaccharides. And some enzymes have been employed to produce low molecular weight polysaccharides and oligosaccharides with verified bioactivities <cite>Cheng2022 Li2021</cite>.

== References ==
<biblio>
#Shen2018 pmid=29355636
#Cao2021 pmid=34421852
#Zhang2019 pmid=31352784
#Zhang2020 pmid=32520542
#Dong2017 pmid=27576198
#Shen2017 pmid=28760444
#Cao2020 pmid=32578425
#Zhang2023 pmid=36746585
#Shen2020 pmid=32849348
#Liu2023 pmid=36746582
#Pei2019 pmid=30248453
#Mei2020 pmid=32747278
#Mei2022a pmid=34893209
#Mei2022b pmid=36395930
#Mei2022c pmid=35830544
#Mei2023 pmid=36924869
#Chen2021 pmid=34420739
#Chen2023 pmid=37059545
#Cheng2022 pmid=35667104
#Li2021 pmid=34415766
#Zhou2024 pmid=39174099
#Mei2023a pmid=37769778
#Mei2023b pmid=38010608
</biblio>


[[Category:Contributors|Chang,Yaoguang]]

User:Yaoguang Chang

2024-10-16T07:56:53Z

Jinhang Zhou:

[[File:Yaoguang Chang.jpg|100px|right]]
Yaoguang Chang obtained his Ph.D. degree from the Ocean University of China and was a visiting scholar at the University of Massachusetts Amherst. At present, he is a professor at the College of Food Science and Engineering, Ocean University of China. His research interests involve the gene-mining and characterization of [[Carbohydrate-active enzymes|CAZymes]] and [[carbohydrate-binding modules]] from marine polysaccharides. By utilizing the enzymes and binding proteins as critical tools, novel identification, quantification, and modification methods of marine polysaccharides were established, which would consequently facilitate the development and application of promising functional polysaccharides from the ocean.
His research group discovered the first member of [[GH168]], [[GH174]], [[PL44]],and [[CBM92]] families, and contributed to the studies related to members of the following families:

*[[GH16]]: κ-carrageenase Cgk16A <cite>Shen2018</cite>, βκ-carrageenase Cgbk16A_Wf <cite>Cao2021</cite>, β-porphyranase Por16A_Wf <cite>Zhang2019</cite>, and β-porphyranase Por16C_Wf <cite>Zhang2020</cite>
*[[GH29]]: fucosidase Alf1_Wf <cite>Dong2017</cite>
*[[GH82]]: ι-carrageenase Cgi82A <cite>Shen2017</cite>
*[[GH86]]: β-agarase Aga86A_Wa <cite>Cao2020 Zhang2023</cite>
*[[GH168]]: endo-1,3-fucanase Fun168A <cite>Shen2020</cite>
*[[GH174]]: endo-1,3-fucanase Fun174A <cite>Liu2023</cite>
*[[PL7]]: alginate lyase Aly7B_Wf <cite>Pei2019</cite>
*[[PL44]]: alginate lyase Aly44A <cite>Zhou2024</cite>
*[[CBM16]]: ABP_Wf (alginate-binding CBM) <cite>Mei2020</cite>
*[[CBM47]]: WfCBM47 (sulfated fucan-binding CBM) <cite>Mei2020a</cite>
*[[CBM70]]: SrCBM70 (hyaluronic acid-binding CBM) <cite>Mei2020b</cite>
*[[CBM92]]: Cgk16A-CBM92 (carrageenan-binding CBM) <cite>Mei2020c</cite>
*CBMnc: Fun174A-CBM (sulfated fucan-binding CBM) <cite>Mei2023</cite>

Some of the above biotechnological tools have been successfully integrated with glycomics <cite>Chen2021 Chen2023</cite>, lateral flow immunoassay <cite>Mei2020b</cite>, and other techniques, and served in the structural and chemical investigation of marine polysaccharides. And some enzymes have been employed to produce low molecular weight polysaccharides and oligosaccharides with verified bioactivities <cite>Cheng2022 Li2021</cite>.

== References ==
<biblio>
#Shen2018 pmid=29355636
#Cao2021 pmid=34421852
#Zhang2019 pmid=31352784
#Zhang2020 pmid=32520542
#Dong2017 pmid=27576198
#Shen2017 pmid=28760444
#Cao2020 pmid=32578425
#Zhang2023 pmid=36746585
#Shen2020 pmid=32849348
#Liu2023 pmid=36746582
#Pei2019 pmid=30248453
#Mei2020 pmid=32747278
#Mei2022a pmid=34893209
#Mei2022b pmid=36395930
#Mei2022c pmid=35830544
#Mei2023 pmid=36924869
#Chen2021 pmid=34420739
#Chen2023 pmid=37059545
#Cheng2022 pmid=35667104
#Li2021 pmid=34415766
#Zhou2024 pmid=39174099
</biblio>


[[Category:Contributors|Chang,Yaoguang]]

User:Yaoguang Chang

2024-10-16T07:56:10Z

Jinhang Zhou:

[[File:Yaoguang Chang.jpg|100px|right]]
Yaoguang Chang obtained his Ph.D. degree from the Ocean University of China and was a visiting scholar at the University of Massachusetts Amherst. At present, he is a professor at the College of Food Science and Engineering, Ocean University of China. His research interests involve the gene-mining and characterization of [[Carbohydrate-active enzymes|CAZymes]] and [[carbohydrate-binding modules]] from marine polysaccharides. By utilizing the enzymes and binding proteins as critical tools, novel identification, quantification, and modification methods of marine polysaccharides were established, which would consequently facilitate the development and application of promising functional polysaccharides from the ocean.
His research group discovered the first member of [[GH168]], [[GH174]],[[PL44]],and [[CBM92]] families, and contributed to the studies related to members of the following families:

*[[GH16]]: κ-carrageenase Cgk16A <cite>Shen2018</cite>, βκ-carrageenase Cgbk16A_Wf <cite>Cao2021</cite>, β-porphyranase Por16A_Wf <cite>Zhang2019</cite>, and β-porphyranase Por16C_Wf <cite>Zhang2020</cite>
*[[GH29]]: fucosidase Alf1_Wf <cite>Dong2017</cite>
*[[GH82]]: ι-carrageenase Cgi82A <cite>Shen2017</cite>
*[[GH86]]: β-agarase Aga86A_Wa <cite>Cao2020 Zhang2023</cite>
*[[GH168]]: endo-1,3-fucanase Fun168A <cite>Shen2020</cite>
*[[GH174]]: endo-1,3-fucanase Fun174A <cite>Liu2023</cite>
*[[PL7]]: alginate lyase Aly7B_Wf <cite>Pei2019</cite>
*[[PL44]]: alginate lyase Aly44A <cite>Zhou2024</cite>
*[[CBM16]]: ABP_Wf (alginate-binding CBM) <cite>Mei2020</cite>
*[[CBM47]]: WfCBM47 (sulfated fucan-binding CBM) <cite>Mei2020a</cite>
*[[CBM70]]: SrCBM70 (hyaluronic acid-binding CBM) <cite>Mei2020b</cite>
*[[CBM92]]: Cgk16A-CBM92 (carrageenan-binding CBM) <cite>Mei2020c</cite>
*CBMnc: Fun174A-CBM (sulfated fucan-binding CBM) <cite>Mei2023</cite>

Some of the above biotechnological tools have been successfully integrated with glycomics <cite>Chen2021 Chen2023</cite>, lateral flow immunoassay <cite>Mei2020b</cite>, and other techniques, and served in the structural and chemical investigation of marine polysaccharides. And some enzymes have been employed to produce low molecular weight polysaccharides and oligosaccharides with verified bioactivities <cite>Cheng2022 Li2021</cite>.

== References ==
<biblio>
#Shen2018 pmid=29355636
#Cao2021 pmid=34421852
#Zhang2019 pmid=31352784
#Zhang2020 pmid=32520542
#Dong2017 pmid=27576198
#Shen2017 pmid=28760444
#Cao2020 pmid=32578425
#Zhang2023 pmid=36746585
#Shen2020 pmid=32849348
#Liu2023 pmid=36746582
#Pei2019 pmid=30248453
#Mei2020 pmid=32747278
#Mei2022a pmid=34893209
#Mei2022b pmid=36395930
#Mei2022c pmid=35830544
#Mei2023 pmid=36924869
#Chen2021 pmid=34420739
#Chen2023 pmid=37059545
#Cheng2022 pmid=35667104
#Li2021 pmid=34415766
#Zhou2024 pmid=39174099
</biblio>


[[Category:Contributors|Chang,Yaoguang]]

User:Jinhang Zhou

2024-10-16T07:55:40Z

Jinhang Zhou:

[[Image:JINHANG ZHOU.png|112px|right]]
Jinhang Zhou is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of polysaccharide lyases. She discovered and characterized the first member of [[PL44]] <cite>Zhou2024</cite>.
*[[PL44]]: alginate lyase Aly44A <cite>Zhou2024</cite>

----

<biblio>
#Zhou2024 pmid=39174099

</biblio>


[[Category:Contributors|Zhou,Jinhang]]

User:Jinhang Zhou

2024-10-16T07:50:55Z

Jinhang Zhou:

[[Image:JINHANG ZHOU.png|112px|right]]
Jinhang Zhou is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of polysaccharide lyases. She discovered and characterized the first member of [[PL44]] <cite>Zhou2024</cite>.
*[[PL44]]: Aly44A <cite>Zhou2024</cite>

----

<biblio>
#Zhou2024 pmid=39174099

</biblio>


[[Category:Contributors|Zhou,Jinhang]]

File:JINHANG ZHOU.png

2024-10-16T07:50:03Z

Jinhang Zhou:

User:Jinhang Zhou

2024-10-16T07:49:25Z

Jinhang Zhou:

[[Image:JINHANG ZHOU.png|154px|right]]
Jinhang Zhou is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of polysaccharide lyases. She discovered and characterized the first member of [[PL44]] <cite>Zhou2024</cite>.
*[[PL44]]: Aly44A <cite>Zhou2024</cite>

----

<biblio>
#Zhou2024 pmid=39174099

</biblio>


[[Category:Contributors|Zhou,Jinhang]]

User:Jinhang Zhou

2024-10-16T07:48:11Z

Jinhang Zhou:

[[Image:JINHANG ZHOU.png|112px|right]]
Jinhang Zhou is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of polysaccharide lyases. She discovered and characterized the first member of [[PL44]] <cite>Zhou2024</cite>.
*[[PL44]]: Aly44A <cite>Zhou2024</cite>

----

<biblio>
#Zhou2024 pmid=39174099

</biblio>


[[Category:Contributors|Zhou,Jinhang]]

User:Jinhang Zhou

2024-10-16T07:35:44Z

Jinhang Zhou:

[[Image:Jinhang Zhou.jpg|295px|right]]
Jinhang Zhou is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of polysaccharide lyases. She discovered and characterized the first member of [[PL44]] <cite>Zhou2024</cite>.
*[[PL44]]: Aly44A <cite>Zhou2024</cite>

----

<biblio>
#Zhou2024 pmid=39174099

</biblio>


[[Category:Contributors|Zhou,Jinhang]]

Polysaccharide Lyase Family 44

2024-10-16T07:27:35Z

Jinhang Zhou:

{{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'''
|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'''
|-
| colspan="2" |{{CAZyDBlink}}PL44.html
|}
</div>


== 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).

== 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 ==
<biblio>
#Zhou2024 pmid=39174099
</biblio>

[[Category:Polysaccharide Lyase Families|PL044]]

Polysaccharide Lyase Family 44

2024-10-16T07:27:03Z

Jinhang Zhou:

{{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'''
|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'''
|-
| colspan="2" |{{CAZyDBlink}}PL44.html
|}
</div>


== 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).

== 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 ==
<biblio>
#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]]

Polysaccharide Lyase Family 44

2024-10-16T07:25:27Z

Jinhang Zhou:

{{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'''
|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'''
|-
| colspan="2" |{{CAZyDBlink}}PL44.html
|}
</div>


== 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).

== 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 ==
<biblio>
#Zhou2024, PMID=39174099
</biblio>
#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]]

Polysaccharide Lyase Family 44

2024-10-16T07:22:10Z

Jinhang Zhou:

{{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'''
|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'''
|-
| colspan="2" |{{CAZyDBlink}}PL44.html
|}
</div>


== 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).

== 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 ==
<biblio>
#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/10.1016/j.carbpol.2024.122474 Download PDF version].
</biblio>

[[Category:Polysaccharide Lyase Families|PL044]]

Polysaccharide Lyase Family 44

2024-10-13T08:47:52Z

Jinhang Zhou:

{{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 ==
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: <cite>DaviesSinnott2008 Cantarel2009</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).

== 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 ==
<biblio>
#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>

[[Category:Polysaccharide Lyase Families|PL044]]

User:Jinhang Zhou

2024-10-09T01:27:14Z

Jinhang Zhou:

[[Image:Jinhang Zhou.jpg|295px|right]]
'''This is an empty template to help you get started with composing your User page.'''

You should begin by opening this page for editing by clicking on the Edit tab above. Your biography goes in this area of the page.

* See [[User:Gerlind_Sulzenbacher]] for an example. You may copy text from this example by opening the page in another browser window and clicking the "Edit" tab.
* Add your publications in the list below using PubMed IDs and cite them in the text like this <cite>Gilbert2008</cite>.
* Please upload a picture of yourself using the "Upload file" link in the Toolbox section of the left menu, and then replace the Image filename with your own.

''More specific help on these steps is available from the links under the "For contributors" section of the left page menu.''

----

<biblio>
#Gilbert2008 pmid=18430603

</biblio>


[[Category:Contributors|Zhou,Jinhang]]

File:Jinhang Zhou.jpg

2024-10-09T01:17:10Z

Jinhang Zhou:

File:Jinhang Zhou.png

2024-10-09T01:15:23Z

Jinhang Zhou:

User:Jinhang Zhou

2024-10-09T01:14:10Z

Jinhang Zhou:

[[Image:Jinhang Zhou.png|200px|right]]
'''This is an empty template to help you get started with composing your User page.'''

You should begin by opening this page for editing by clicking on the Edit tab above. Your biography goes in this area of the page.

* See [[User:Gerlind_Sulzenbacher]] for an example. You may copy text from this example by opening the page in another browser window and clicking the "Edit" tab.
* Add your publications in the list below using PubMed IDs and cite them in the text like this <cite>Gilbert2008</cite>.
* Please upload a picture of yourself using the "Upload file" link in the Toolbox section of the left menu, and then replace the Image filename with your own.

''More specific help on these steps is available from the links under the "For contributors" section of the left page menu.''

----

<biblio>
#Gilbert2008 pmid=18430603

</biblio>


[[Category:Contributors|Zhou,Jinhang]]

File:Cazy.png

2024-10-09T01:12:12Z

Jinhang Zhou:

User:Jinhang Zhou

2024-10-09T01:09:51Z

Jinhang Zhou:

[[Image:cazy.png|200px|right]]
'''This is an empty template to help you get started with composing your User page.'''

You should begin by opening this page for editing by clicking on the Edit tab above. Your biography goes in this area of the page.

* See [[User:Gerlind_Sulzenbacher]] for an example. You may copy text from this example by opening the page in another browser window and clicking the "Edit" tab.
* Add your publications in the list below using PubMed IDs and cite them in the text like this <cite>Gilbert2008</cite>.
* Please upload a picture of yourself using the "Upload file" link in the Toolbox section of the left menu, and then replace the Image filename with your own.

''More specific help on these steps is available from the links under the "For contributors" section of the left page menu.''

----

<biblio>
#Gilbert2008 pmid=18430603

</biblio>


[[Category:Contributors|Zhou,Jinhang]]