Polysaccharide Lyase Family 31 - Revision history

Harry Brumer at 22:33, 1 October 2024

2024-10-01T22:33:02Z

Marie-Line Garron at 15:42, 23 August 2024

2024-08-23T15:42:32Z

Marie-Line Garron at 14:57, 23 August 2024

2024-08-23T14:57:48Z

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:15:21Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer at 01:06, 13 June 2020

2020-06-13T01:06:58Z

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

2020-06-13T01:02:30Z

Created page with " {{UnderConstruct..."

New page

{{UnderConstruction}}
* [[Author]]: ^^^Marie-Line Garron^^^
* [[Responsible Curator]]: ^^^Marie-Line Garron^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL31'''
|-
|'''3D Structure'''
|
|-
|'''Mechanism'''
|
|-
|'''Charge neutraliser'''
|
|-
|'''Active site residues'''
|
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL31.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:Glycoside Hydrolase Families|PL031]]

@@ Line 32: / Line 32: @@
 == Substrate specificities ==
-The PL31 family is mainly a bacterial family distantly related to the PL41 family ([http://www.cazy.org/PL31.html PL31]) <cite>Drula2022</cite>. The first activities were demonstrated against poly-glucuronan for ''Saccharophagus degradans 2-40'' (ABD82242.1) and ''Streptomyces hygroscopicus subsp. jinggangensis'' (AGF62897.1) ([https://www.enzyme-database.org/query.php?ec=4.2.2.14 EC 4.2.2.14]) <cite>Helbert2019</cite>. Shortly afterwards, another PL31 member with a different function was characterized. PsAly, from ''Paenibacillus sp. FPU-7'', is an endo-alginate lyase specific for polymannuronate ([https://www.enzyme-database.org/query.php?ec=4.2.2.3 EC 4.2.2.3])  <cite>Itoh2019</cite>. The poly-M specific alginate lyase function was confirmed by the characterization of paeh-aly, belonging to ''Paenibacillus ehimensis'' <cite>Wang2023</cite>.  The two publications on poly-M alginate lyases also reported a significant increase in activity in the presence of divalent cations, mainly Mg<sup>2+</sup>  <cite>Itoh2019 Wang2023</cite>.
+The PL31 family is mainly a bacterial family distantly related to the [[PL41]] family. The first activities were demonstrated against poly-glucuronan for ''Saccharophagus degradans 2-40'' (ABD82242.1) and ''Streptomyces hygroscopicus subsp. jinggangensis'' (AGF62897.1) ([https://www.enzyme-database.org/query.php?ec=4.2.2.14 EC 4.2.2.14]) <cite>Helbert2019</cite>. Shortly afterwards, another PL31 member with a different function was characterized. PsAly, from ''Paenibacillus sp. FPU-7'', is an endo-alginate lyase specific for polymannuronate ([https://www.enzyme-database.org/query.php?ec=4.2.2.3 EC 4.2.2.3])  <cite>Itoh2019</cite>. The poly-M specific alginate lyase function was confirmed by the characterization of paeh-aly, belonging to ''Paenibacillus ehimensis'' <cite>Wang2023</cite>.  The two publications on poly-M alginate lyases also reported a significant increase in activity in the presence of divalent cations, mainly Mg<sup>2+</sup>  <cite>Itoh2019 Wang2023</cite>.
 == Kinetics and Mechanism ==
@@ Line 53: / Line 53: @@
 == References ==
 <biblio>
 #Helbert2019 pmid=30850540
 #Itoh2019 pmid=31619701

← Older revision		Revision as of 01:06, 13 June 2020
Line 59:		Line 59:
	</biblio>		</biblio>

−	[[Category:~~Glycoside Hydrolase~~ Families\|PL031]]	+	[[Category:Polysaccharide Lyase Families\|PL031]]

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Marie-Line Garron|Marie-Line Garron]]
 * [[Responsible Curator]]:  [[User:Marie-Line Garron|Marie-Line Garron]]

@@ Line 12: / Line 12: @@
 |-
 |'''3D Structure'''
+|Right handed &beta;-helix
 |-
 |'''Mechanism'''
+|&beta;-elimination
 |-
 |'''Charge neutraliser'''
+|Divalent cation (based on docking)
 |-
 |'''Active site residues'''
+|Lysine (base) and Tyrosine (acid) (mutagenesis and docking)
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
@@ Line 32: / Line 32: @@
 == Substrate specificities ==
-Content is to be added here.
+The PL31 family is mainly a bacterial family distantly related to the PL41 family ([http://www.cazy.org/PL31.html PL31]) <cite>Drula2022</cite>. The first activities were demonstrated against poly-glucuronan for ''Saccharophagus degradans 2-40'' (ABD82242.1) and ''Streptomyces hygroscopicus subsp. jinggangensis'' (AGF62897.1) ([https://www.enzyme-database.org/query.php?ec=4.2.2.14 EC 4.2.2.14]) <cite>Helbert2019</cite>. Shortly afterwards, another PL31 member with a different function was characterized. PsAly, from ''Paenibacillus sp. FPU-7'', is an endo-alginate lyase specific for polymannuronate ([https://www.enzyme-database.org/query.php?ec=4.2.2.3 EC 4.2.2.3])  <cite>Itoh2019</cite>. The poly-M specific alginate lyase function was confirmed by the characterization of paeh-aly, belonging to ''Paenibacillus ehimensis'' <cite>Wang2023</cite>.  The two publications on poly-M alginate lyases also reported a significant increase in activity in the presence of divalent cations, mainly Mg<sup>2+</sup>  <cite>Itoh2019 Wang2023</cite>.
-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...)''
+== Kinetics and Mechanism ==
-In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.
-== Kinetics and Mechanism ==
+== Family Firsts ==
-Content is to be added here.
+;First desciption of catalytic activity: Glucuronan lyase was the first activity reported for the family PL31 <cite>Helbert2019</cite>.
-== Catalytic Residues ==
+;First charge neutralizer identification: Based on the influence of cations on activity and the docking experiments, Itoh and co-workers hypothesised that divalent cations could be the neutralizer <cite>Itoh2019</cite>.
-== Three-dimensional structures ==
+;First Brønstead acid and base residue identification: The total loss of activity when PsAly is mutated on Y184 and K221, confirms their crucial role in catalysis. The base and acid functions were assigned on the basis of docking: Lys the base and Tyr the acid <cite>Itoh2019</cite>.
-== Family Firsts ==
+;First 3-D structure: The structure of the poly-M specific alginate lyase, PSAly, was the first solved by X-ray diffraction at 0.89Å resolution ([https://www.rcsb.org/structure/6KFN PDB 6KFN]) <cite>Itoh2019</cite>.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Drula2022 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].
+#Helbert2019 pmid=30850540
 </biblio>
 [[Category:Polysaccharide Lyase Families|PL031]]