Glycoside Hydrolase Family 168 - Revision history

Harry Brumer at 19:23, 18 June 2023

2023-06-18T19:23:06Z

Harry Brumer: /* Substrate specificities */

2023-06-18T19:19:15Z

Substrate specificities

Jingjing Shen at 14:05, 18 June 2023

2023-06-18T14:05:41Z

Jingjing Shen at 14:02, 18 June 2023

2023-06-18T14:02:45Z

Jingjing Shen at 14:02, 18 June 2023

2023-06-18T14:02:09Z

Jingjing Shen at 13:59, 18 June 2023

2023-06-18T13:59:26Z

Jingjing Shen at 13:57, 18 June 2023

2023-06-18T13:57:48Z

Jingjing Shen at 13:49, 18 June 2023

2023-06-18T13:49:39Z

Harry Brumer: Added Jingjing Shen as Author

2023-01-06T19:57:24Z

Added Jingjing Shen as Author

Harry Brumer at 19:53, 5 January 2023

2023-01-05T19:53:57Z

@@ Line 34: / Line 34: @@
 == Kinetics and Mechanism ==
-As mentioned in the report, Fun168A exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. The transglycosylating activity of Fun168A implied its retaining mechanism in catalysis <cite>Shen2020</cite>.
+''W. funcanilytica'' Fun168A exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. This transglycosylating activity implied a  [[retaining]] mechanism of catalysis <cite>Shen2020</cite>.
 == Catalytic Residues ==
-Multiple sequence alignments of GH168 homologues showed that D206 and E264 in Fun168A were strictly conserved in all sequences. Two single-site mutants D206E and E264Q were established, expressed and identified in the report. These two mutants were all inactive on Ib-FUC, indicating that D206 and E264 were critical for the activity of Fun168A <cite>Shen2020</cite>.
+Multiple sequence alignments of GH168 homologues showed that D206 and E264 in Fun168A were strictly conserved in all sequences. Two single-site mutants of ''W. funcanilytica'' Fun168A, D206E and E264Q, were inactive on Ib-FUC, indicating that D206 and E264 were critical for activity <cite>Shen2020</cite>.
-[[File:catalytic residues.png|thumb|'''Figure 2. Multiple sequence alignments of residues in GH168 homologues.''' The strictly conserved residues in all sequences were indicated with black triangles.]]
+[[File:catalytic residues.png|thumb|'''Figure 2. Multiple sequence alignments of residues in GH168 homologues.''' The strictly conserved residues in all sequences are indicated with black triangles.]]
 == Three-dimensional structures ==
-No three-dimensional structure has been solved in this glycoside hydrolase family at present.
+No three-dimensional structure has been solved in this family at present.
 == Family Firsts ==

@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-Members of [[GH168|glycoside hydrolase family 168]] have been shown to exhibit α-1,3-L-fucanase activity. The first member of this family, Fun168A from a marine bacterium ''Wenyingzhuangia funcanilytica'' CZ1127<sup>T</sup>, specifically hydrolyze the α-1,3- L-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber ''Isostichopus badionotus'' in a random endo-acting manner. Meanwhile, five homologues of Fun168A display activities toward sulfated fucan from ''Isostichopus badionotus'', namely WP_081987558.1, WP_068826447.1, WP_068826442.1, OHE80969.1 and WP_083194720.1 <cite>Shen2020</cite>.
+Members of GH168 have been shown to exhibit α-1,3-L-fucanase activity. The first member of this family, Fun168A from a marine bacterium ''Wenyingzhuangia funcanilytica'' CZ1127<sup>T</sup>, specifically hydrolyzes the α-1,3- L-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber ''Isostichopus badionotus'' in a random endo-acting manner. Meanwhile, [http://www.cazy.org/GH168_characterized.html five homologues of Fun168A display activities toward sulfated fucan] from ''Isostichopus badionotus'' <cite>Shen2020</cite>.
 [[File:Tree of GH168.png|thumb|'''Figure 1. The phylogenetic tree of GH168 homologues.''' Sequences comfirmed to exhibit α-1,3-L-fucanase activity were in red.]]

@@ 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:Jingjing Shen|Jingjing Shen]]
 * [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]

@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-Members of [[GH168|glycoside hydrolase family 168]] have been shown to exhibit α-1,3-L-fucanase activity. The first member of this family, Fun168A from a marine bacterium ''Wenyingzhuangia funcanilytica'' CZ1127<sup>T</sup>, specifically hydrolyze the α-1,3- L-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber ''Isostichopus badionotus'' in a random endo-acting manner <cite>Shen2020</cite>. Meanwhile, five homologues of Fun168A display activities toward sulfated fucan from ''Isostichopus badionotus'', namely WP_081987558.1, WP_068826447.1, WP_068826442.1, OHE80969.1 and WP_083194720.1.
+Members of [[GH168|glycoside hydrolase family 168]] have been shown to exhibit α-1,3-L-fucanase activity. The first member of this family, Fun168A from a marine bacterium ''Wenyingzhuangia funcanilytica'' CZ1127<sup>T</sup>, specifically hydrolyze the α-1,3- L-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber ''Isostichopus badionotus'' in a random endo-acting manner. Meanwhile, five homologues of Fun168A display activities toward sulfated fucan from ''Isostichopus badionotus'', namely WP_081987558.1, WP_068826447.1, WP_068826442.1, OHE80969.1 and WP_083194720.1 <cite>Shen2020</cite>.
 [[File:Tree of GH168.png|thumb|'''Figure 1. The phylogenetic tree of GH168 homologues.''' Sequences comfirmed to exhibit α-1,3-L-fucanase activity were in red.]]

@@ Line 34: / Line 34: @@
 == Kinetics and Mechanism ==
-As mentioned in the report, Fun168A exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. The transglycosylating activity of Fun168A implied its retaining mechanism in catalysis.
+As mentioned in the report, Fun168A exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. The transglycosylating activity of Fun168A implied its retaining mechanism in catalysis <cite>Shen2020</cite>.
 == Catalytic Residues ==
-Multiple sequence alignments of GH168 homologues showed that D206 and E264 in Fun168A were strictly conserved in all sequences. Two single-site mutants D206E and E264Q were established, expressed and identified in the report. These two mutants were all inactive on Ib-FUC, indicating that D206 and E264 were critical for the activity of Fun168A.
+Multiple sequence alignments of GH168 homologues showed that D206 and E264 in Fun168A were strictly conserved in all sequences. Two single-site mutants D206E and E264Q were established, expressed and identified in the report. These two mutants were all inactive on Ib-FUC, indicating that D206 and E264 were critical for the activity of Fun168A <cite>Shen2020</cite>.
 [[File:catalytic residues.png|thumb|'''Figure 2. Multiple sequence alignments of residues in GH168 homologues.''' The strictly conserved residues in all sequences were indicated with black triangles.]]

@@ Line 16: / Line 16: @@
 |-
 |'''Mechanism'''
-|retaining/inverting
+|retaining
 |-
 |'''Active site residues'''
-|known/not known
+|not known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-Members of [[GH168|glycoside hydrolase family 168]] have been shown to exhibit α-1,3-L-fucanase activity. The first member of this family, Fun168A from a marine bacterium Wenyingzhuangia funcanilytica CZ1127T, specifically hydrolyze the α-1,3- L-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber Isostichopus badionotus in a random endo-acting manner <cite>Shen2020</cite>. Meanwhile, five homologues of Fun168A display activities toward sulfated fucan from Isostichopus badionotus, namely WP_081987558.1, WP_068826447.1, WP_068826442.1, OHE80969.1 and WP_083194720.1.
+Members of [[GH168|glycoside hydrolase family 168]] have been shown to exhibit α-1,3-L-fucanase activity. The first member of this family, Fun168A from a marine bacterium ''Wenyingzhuangia funcanilytica'' CZ1127<sup>T</sup>, specifically hydrolyze the α-1,3- L-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber Isostichopus badionotus in a random endo-acting manner <cite>Shen2020</cite>. Meanwhile, five homologues of Fun168A display activities toward sulfated fucan from ''Isostichopus badionotus'', namely WP_081987558.1, WP_068826447.1, WP_068826442.1, OHE80969.1 and WP_083194720.1.
 == Kinetics and Mechanism ==
@@ Line 37: / Line 38: @@
 == Catalytic Residues ==
 Multiple sequence alignments of GH168 homologues showed that D206 and E264 in Fun168A were strictly conserved in all sequences. Two single-site mutants D206E and E264Q were established, expressed and identified in the report. These two mutants were all inactive on Ib-FUC, indicating that D206 and E264 were critical for the activity of Fun168A.
 == Three-dimensional structures ==

@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-Content is to be added here.
+Members of [[GH168|glycoside hydrolase family 168]] have been shown to exhibit α-1,3-L-fucanase activity. The first member of this family, Fun168A from a marine bacterium Wenyingzhuangia funcanilytica CZ1127T, specifically hydrolyze the α-1,3- L-fucoside bonds between 2-O-sulfated and non-sulfated fucose residues in the sulfated fucan from sea cucumber Isostichopus badionotus in a random endo-acting manner <cite>Shen2020</cite>. Meanwhile, five homologues of Fun168A display activities toward sulfated fucan from Isostichopus badionotus, namely WP_081987558.1, WP_068826447.1, WP_068826442.1, OHE80969.1 and WP_083194720.1.
 == Kinetics and Mechanism ==
-Content is to be added here.
+As mentioned in the report, Fun168A exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. The transglycosylating activity of Fun168A implied its retaining mechanism in catalysis.
 == Catalytic Residues ==
-Content is to be added here.
+Multiple sequence alignments of GH168 homologues showed that D206 and E264 in Fun168A were strictly conserved in all sequences. Two single-site mutants D206E and E264Q were established, expressed and identified in the report. These two mutants were all inactive on Ib-FUC, indicating that D206 and E264 were critical for the activity of Fun168A.
 == Three-dimensional structures ==
-Content is to be added here.
+No three-dimensional structure has been solved in this glycoside hydrolase family at present.
 == Family Firsts ==
-;First stereochemistry determination: Content is to be added here.
+;First stereochemistry determination: Not yet identified.
-;First catalytic nucleophile identification: Content is to be added here.
+;First catalytic nucleophile identification: Not yet identified.
-;First general acid/base residue identification: Content is to be added here.
+;First general acid/base residue identification: Not yet identified.
-;First 3-D structure: Content is to be added here.
+;First 3-D structure: Not yet identified.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Shen2020 pmid=32849348
 </biblio>
 <!-- Do not delete this Category tag -->
 [[Category:Glycoside Hydrolase Families|GH168]]

← Older revision		Revision as of 19:53, 5 January 2023
Line 1:		Line 1:
−	{{~~UnassignedPage~~}}	+	<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
		+	{{UnderConstruction}}
		+	* [[Author]]:

		+	* [[Responsible Curator]]: [[User:Yaoguang Chang\|Yaoguang Chang]]

		+	----
		+
		+	<!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
		+	<div style="float:right">
		+	{\| {{Prettytable}}
		+	\|-
		+	\|{{Hl2}} colspan="2" align="center" \|'''Glycoside Hydrolase Family GH168'''
		+	\|-
		+	\|'''Clan'''
		+	\|GH-x
		+	\|-
		+	\|'''Mechanism'''
		+	\|retaining/inverting
		+	\|-
		+	\|'''Active site residues'''
		+	\|known/not known
		+	\|-
		+	\|{{Hl2}} colspan="2" align="center" \|'''CAZy DB link'''
		+	\|-
		+	\| colspan="2" \|{{CAZyDBlink}}GH168.html
		+	\|}
		+	</div>
		+	<!-- This is the end of the table -->
		+
		+
		+	== Substrate specificities ==
		+	Content is to be added here.
		+
		+	Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase 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>
		+
		+	<!-- Do not delete this Category tag -->
	[[Category:Glycoside Hydrolase Families\|GH168]]		[[Category:Glycoside Hydrolase Families\|GH168]]