Glycoside Hydrolase Family 140 - Revision history

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

2021-12-18T21:14:12Z

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

Alan Cartmell at 19:18, 11 May 2020

2020-05-11T19:18:39Z

Alan Cartmell at 19:17, 11 May 2020

2020-05-11T19:17:16Z

Alan Cartmell at 19:15, 11 May 2020

2020-05-11T19:15:27Z

Harry Brumer at 19:23, 27 January 2020

2020-01-27T19:23:56Z

Harry Brumer at 19:21, 27 January 2020

2020-01-27T19:21:20Z

Alan Cartmell at 16:04, 25 January 2020

2020-01-25T16:04:59Z

Alan Cartmell at 15:17, 25 January 2020

2020-01-25T15:17:47Z

Alan Cartmell at 15:17, 25 January 2020

2020-01-25T15:17:00Z

Alan Cartmell at 15:15, 25 January 2020

2020-01-25T15:15:33Z

@@ 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]]: ^^^Alan Cartmell^^^
+* [[Author]]: [[User:Alan Cartmell|Alan Cartmell]]
-* [[Responsible Curator]]:  ^^^Alan Cartmell^^^
+* [[Responsible Curator]]:  [[User:Alan Cartmell|Alan Cartmell]]
 ----

@@ Line 12: / Line 12: @@
 |-
 |'''Clan'''
-|No clan assigned
+|None
 |-
 |'''Mechanism'''

@@ 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]]: ^^^Alan Cartmell^^^
-* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
+* [[Responsible Curator]]:  ^^^Alan Cartmell^^^
 ----
@@ Line 12: / Line 12: @@
 |-
 |'''Clan'''
-|GH-x
+|No clan assigned
 |-
 |'''Mechanism'''

@@ Line 52: / Line 52: @@
 #McKee2012 pmid=22492980
 #Cartmell2011 pmid=21339299
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH140]]

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur before BT1012 can act<cite>Ndeh2017</cite>.
+Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur before BT1012 can act <cite>Ndeh2017</cite>.
 == Kinetics and Mechanism ==
-GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism<cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product.
+GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism <cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product.
 == Catalytic Residues ==
-The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively<cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.
+The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively <cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.
 == Three-dimensional structures ==
-GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices<cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in [[GH43]] enzymes <cite>McKee2012 Cartmell2011</cite>.
+GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices <cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in [[GH43]] enzymes <cite>McKee2012 Cartmell2011</cite>.
 == Family Firsts ==
-;First stereochemistry determination: Methanolysis experiments suggest a retaining mechanism<cite>Ndeh2017</cite>.
+;First stereochemistry determination: Methanolysis experiments suggest a retaining mechanism <cite>Ndeh2017</cite>.
 ;First catalytic nucleophile identification: Not known.
 ;First general acid/base residue identification: Not Known.

@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices<cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes<cite>McKee2012 Cartmell2011</cite>.
+GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices<cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in [[GH43]] enzymes <cite>McKee2012 Cartmell2011</cite>.
 == Family Firsts ==
@@ Line 44: / Line 44: @@
 ;First catalytic nucleophile identification: Not known.
 ;First general acid/base residue identification: Not Known.
-;First 3-D structure: BT1012 from bacteroides thetaiotaomicron<cite>Ndeh2017</cite>.
+;First 3-D structure: BT1012 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.
 == References ==

@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes.
+GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes<cite>McKee2012 Cartmell2011</cite>.
 == Family Firsts ==
@@ Line 51: / Line 51: @@
 #Ndeh2017 pmid=28329766
 #Shallom2002 pmid=12221104
 #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. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].