Glycoside Hydrolase Family 151 - Revision history

Birgitte Zeuner at 11:19, 20 May 2022

2022-05-20T11:19:17Z

Birgitte Zeuner: wording

2022-05-20T11:18:08Z

wording

Birgitte Zeuner: 3-D structure available

2022-05-20T11:17:02Z

3-D structure available

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

2021-12-18T21:16:52Z

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

Birgitte Zeuner: Curator Approved

2020-06-13T17:32:38Z

Curator Approved

Birgitte Zeuner at 08:48, 12 June 2020

2020-06-12T08:48:02Z

Harry Brumer: added EC link

2020-06-04T16:28:52Z

added EC link

David Teze at 10:17, 4 June 2020

2020-06-04T10:17:46Z

David Teze at 10:17, 4 June 2020

2020-06-04T10:17:18Z

Birgitte Zeuner at 09:55, 4 June 2020

2020-06-04T09:55:38Z

@@ Line 39: / Line 39: @@
 == Three-dimensional structures ==
-The first solved structure in GH151 was that of α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'' <cite>Kovalova2022</cite>. It revealed a tetrameric structure with active site complementation by His503.
+The first solved structure in GH151 was that of α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus''. It revealed a tetrameric structure with active site complementation by His503 <cite>Kovalova2022</cite>.
 == Family Firsts ==

@@ Line 36: / Line 36: @@
 == Catalytic Residues ==
-In the α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'', Glu235 was assigned as catalytic acid/base and Asp154 as catalytic nucleophile following a combination of mutational, structural, docking, and QM/MM studies <cite>Kovalova2022</cite>. Initially, both Asp9 and Asp154 were investigated as putative nucleophiles. However, docking studies combined with the fact that the variant D9N performed well in transglycosylation <cite>Teze2021</cite> indicates that its role is in substrate binding <cite>Kovalova2022</cite>.
+In the α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'', Glu235 was assigned as catalytic acid/base and Asp154 as catalytic nucleophile following a combination of mutational, structural, docking, and QM/MM studies <cite>Kovalova2022</cite>. Initially, both Asp9 and Asp154 were investigated as putative nucleophiles. However, docking studies combined with the fact that the variant D9N performed well in transglycosylation <cite>Teze2021</cite> indicated that the role of Asp9 is in substrate binding <cite>Kovalova2022</cite>.
 == Three-dimensional structures ==

@@ Line 17: / Line 17: @@
 |-
 |'''Active site residues'''
-|Not known
+|Known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
@@ Line 33: / Line 33: @@
 == Kinetics and Mechanism ==
-The catalytic mechanism of GH151 has not been determined, but based on reports that two members of GH151 can catalyze transglycosylation using ''p''NP-α-L-Fuc as donor substrate <cite>Benesova2015 Lezyk2016</cite>, a retaining mechanism has been inferred.
+The catalytic mechanism of GH151 has not been determined, but based on reports that two members of GH151 can catalyze transglycosylation using ''p''NP-α-L-Fuc or CNP-α-L-Fuc as donor substrate <cite>Benesova2015 Lezyk2016 Teze2021</cite>, a retaining mechanism has been inferred.
 == Catalytic Residues ==
-The catalytic residues of GH151 are unknown.
+In the α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'', Glu235 was assigned as catalytic acid/base and Asp154 as catalytic nucleophile following a combination of mutational, structural, docking, and QM/MM studies <cite>Kovalova2022</cite>. Initially, both Asp9 and Asp154 were investigated as putative nucleophiles. However, docking studies combined with the fact that the variant D9N performed well in transglycosylation <cite>Teze2021</cite> indicates that its role is in substrate binding <cite>Kovalova2022</cite>.
 == Three-dimensional structures ==
-No three-dimensional structures have been solved for GH151.
+The first solved structure in GH151 was that of α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'' <cite>Kovalova2022</cite>. It revealed a tetrameric structure with active site complementation by His503.
 == Family Firsts ==
 ;First stereochemistry determination: Not yet identified.
-;First catalytic nucleophile identification: Not yet identified.
+;First catalytic nucleophile identification: Asp154 in α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'' <cite>Kovalova2022</cite>.
-;First general acid/base residue identification: Not yet identified.
+;First general acid/base residue identification: Glu235 in α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'' <cite>Kovalova2022</cite>.
-;First 3-D structure: Not yet solved.
+;First 3-D structure: The 3-D structure of α-L-fucosidase isoenzyme 2 from ''Paenibacillus thiaminolyticus'' <cite>Kovalova2022</cite>.
 == References ==
@@ Line 53: / Line 53: @@
 #Benesova2015 pmid=26013545
 #Lezyk2016 pmid=26800369
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH151]]

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Casper Wilkens^^^, ^^^David Teze^^^, and ^^^Birgitte Zeuner^^^
+* [[Author]]: [[User:Casper Wilkens|Casper Wilkens]], [[User:David Teze|David Teze]], and [[User:Birgitte Zeuner|Birgitte Zeuner]]
-* [[Responsible Curator]]:  ^^^Birgitte Zeuner^^^
+* [[Responsible Curator]]:  [[User:Birgitte Zeuner|Birgitte Zeuner]]
 ----

@@ Line 1: / Line 1: @@
-<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
+{{CuratorApproved}}
 * [[Author]]: ^^^Casper Wilkens^^^, ^^^David Teze^^^, and ^^^Birgitte Zeuner^^^
 * [[Responsible Curator]]:  ^^^Birgitte Zeuner^^^

@@ Line 30: / Line 30: @@
 Members of [[GH151]] are bacterial enzymes presenting α-L-fucosidase activity ([{{EClink}}3.2.1.51 EC 3.2.1.51]) <cite>Sela2012 Benesova2015 Lezyk2016</cite>. Activity has been observed on 4-nitrophenyl-α-L-fucopyranoside (''p''NP-α-L-Fuc) <cite>Benesova2015 Lezyk2016</cite> and on 2-chloro-4-nitrophenyl-α-L-fucopyranoside (CNP-α-L-Fuc) <cite>Sela2012</cite>. GH151 α-L-fucosidases are reportedly unable to catalyze hydrolysis of human milk oligosaccharide structures 2'-fucosyllactose (2'FL) and 3-fucosyllactose (3FL) <cite>Sela2012 Lezyk2016</cite>, but slight activity has been observed on the blood group H antigen disaccharide Fuc-α-1,2-Gal <cite>Sela2012</cite>. No activity was observed on fucosylated xyloglucan <cite>Lezyk2016</cite>.
-The first characterized members of GH151 were perceived as members of [[GH29]] due to their α-L-fucosidase activity <cite>Sela2012 Lezyk2016</cite>. However, phylogenetic analysis and sequence alignment revealed poor homology to GH29 <cite>Sela2012 Lezyk2016</cite>. Based on the low sequence similarity to GH29, it was suggested that a new GH family be created <cite>Benesova2015</cite>. Sequence homology to β-galactosidase trimerization domains has been reported <cite>Sela2012 Lezyk2016</cite>. Consequently, one GH151 α-L-fucosidase was tested for activity on ''p''NP-β-D-Gal, ''p''NP-β-D-Glc, and ''p''NP-β-D-Lac, but none was observed <cite>Lezyk2016</cite>.
+The first characterized members of GH151 were perceived as members of [[GH29]] due to their α-L-fucosidase activity <cite>Sela2012 Lezyk2016</cite>. However, phylogenetic analysis and sequence alignment revealed poor homology to GH29 <cite>Sela2012 Lezyk2016</cite>. Based on the low sequence similarity to GH29, it was suggested that a new GH family be created <cite>Benesova2015</cite>. Sequence homology to [[GH42]] β-galactosidase trimerization domains has been reported <cite>Sela2012 Lezyk2016</cite>. Consequently, one GH151 α-L-fucosidase was tested for activity on ''p''NP-β-D-Gal, ''p''NP-β-D-Glc, and ''p''NP-β-D-Lac, but none was observed <cite>Lezyk2016</cite>.
 == Kinetics and Mechanism ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-Members of [[GH151]] are bacterial enzymes presenting α-L-fucosidase activity (EC 3.2.1.51) <cite>Sela2012 Benesova2015 Lezyk2016</cite>. Activity has been observed on 4-nitrophenyl-α-L-fucopyranoside (''p''NP-α-L-Fuc) <cite>Benesova2015 Lezyk2016</cite> and on 2-chloro-4-nitrophenyl-α-L-fucopyranoside (CNP-α-L-Fuc) <cite>Sela2012</cite>. GH151 α-L-fucosidases are reportedly unable to catalyze hydrolysis of human milk oligosaccharide structures 2'-fucosyllactose (2'FL) and 3-fucosyllactose (3FL) <cite>Sela2012 Lezyk2016</cite>, but slight activity has been observed on the blood group H antigen disaccharide Fuc-α-1,2-Gal <cite>Sela2012</cite>. No activity was observed on fucosylated xyloglucan <cite>Lezyk2016</cite>.
+Members of [[GH151]] are bacterial enzymes presenting α-L-fucosidase activity ([{{EClink}}3.2.1.51 EC 3.2.1.51]) <cite>Sela2012 Benesova2015 Lezyk2016</cite>. Activity has been observed on 4-nitrophenyl-α-L-fucopyranoside (''p''NP-α-L-Fuc) <cite>Benesova2015 Lezyk2016</cite> and on 2-chloro-4-nitrophenyl-α-L-fucopyranoside (CNP-α-L-Fuc) <cite>Sela2012</cite>. GH151 α-L-fucosidases are reportedly unable to catalyze hydrolysis of human milk oligosaccharide structures 2'-fucosyllactose (2'FL) and 3-fucosyllactose (3FL) <cite>Sela2012 Lezyk2016</cite>, but slight activity has been observed on the blood group H antigen disaccharide Fuc-α-1,2-Gal <cite>Sela2012</cite>. No activity was observed on fucosylated xyloglucan <cite>Lezyk2016</cite>.
 The first characterized members of GH151 were perceived as members of [[GH29]] due to their α-L-fucosidase activity <cite>Sela2012 Lezyk2016</cite>. However, phylogenetic analysis and sequence alignment revealed poor homology to GH29 <cite>Sela2012 Lezyk2016</cite>. Based on the low sequence similarity to GH29, it was suggested that a new GH family be created <cite>Benesova2015</cite>. Sequence homology to β-galactosidase trimerization domains has been reported <cite>Sela2012 Lezyk2016</cite>. Consequently, one GH151 α-L-fucosidase was tested for activity on ''p''NP-β-D-Gal, ''p''NP-β-D-Glc, and ''p''NP-β-D-Lac, but none was observed <cite>Lezyk2016</cite>.