Glycoside Hydrolase Family 30 - Revision history

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

2021-12-18T21:16:07Z

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

Harry Brumer: fixed CAZyDB link

2012-06-28T23:41:14Z

fixed CAZyDB link

Harry Brumer: fixed broken refs. in Family Firsts

2012-06-28T23:40:19Z

fixed broken refs. in Family Firsts

Harry Brumer: /* Family Firsts */ fixed font formatting

2012-06-28T23:38:05Z

Family Firsts: fixed font formatting

Harry Brumer: Added Franz as an author for family classification contribution

2010-11-09T20:09:11Z

Added Franz as an author for family classification contribution

Harry Brumer: /* Family Classification */

2010-11-07T18:36:40Z

Family Classification

Franz St. John at 22:15, 5 November 2010

2010-11-05T22:15:14Z

Franz St. John at 22:08, 5 November 2010

2010-11-05T22:08:00Z

Franz St. John at 21:27, 5 November 2010

2010-11-05T21:27:29Z

Franz St. John at 21:08, 5 November 2010

2010-11-05T21:08:30Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]s: [[User:Brian Rempel|Brian Rempel]] and ^^^Franz St. John^^^
+* [[Author]]s: [[User:Brian Rempel|Brian Rempel]] and [[User:Franz St. John|Franz St. John]]
 * [[Responsible Curator]]:  [[User:Steve Withers|Stephen Withers]]
 ----

@@ Line 22: / Line 22: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH30.html
+| colspan="2" |{{CAZyDBlink}}GH30.html
 |}
 </div>

@@ Line 43: / Line 43: @@
 ==Family Firsts==
-;First [[catalytic nucleophile]] identification: Human &beta;-glucocerebrosidase by 2-fluoroglucose labelling <cite>#1</cite>
+;First [[catalytic nucleophile]] identification: Human &beta;-glucocerebrosidase by 2-fluoroglucose labelling <cite>miao1994</cite>
-;First 3-D structure of a GH30 enzyme: Human &beta;-glucocerebrosidase <cite>#2</cite>
+;First 3-D structure of a GH30 enzyme: Human &beta;-glucocerebrosidase <cite>dvir2003</cite>
 ==References==

@@ Line 43: / Line 43: @@
 ==Family Firsts==
-;'''First [[catalytic nucleophile]] identification'''
+;First [[catalytic nucleophile]] identification: Human &beta;-glucocerebrosidase by 2-fluoroglucose labelling <cite>#1</cite>
-:Human &beta;-glucocerebrosidase by 2-fluoroglucose labelling <cite>#1</cite>
+;First 3-D structure of a GH30 enzyme: Human &beta;-glucocerebrosidase <cite>#2</cite>
 ==References==

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: [[User:Brian Rempel|Brian Rempel]]
+* [[Author]]s: [[User:Brian Rempel|Brian Rempel]] and ^^^Franz St. John^^^
 * [[Responsible Curator]]:  [[User:Steve Withers|Stephen Withers]]
 ----

@@ Line 27: / Line 27: @@
 ==Family Classification==
-[[GH30]] classification has recently been revised <cite>stjohn2010</cite>. As had been suggested in several reports with respect to glucuronoxylan xylanohydrolases (previously of [[GH5]]) <cite>brumshtein2006,haegeman2009,keen1996,larson2003, mitreva-dautova2006</cite>, these enzymes through sequence analysis appear to be more like enzymes of [[GH30]]. In consideration of these observation the new classification employed phylogenetics, primary amino acid sequence and structure analysis to show that the glucuronoxylan xylanohydrolase in question as well as several other enzyme groups classified as [[GH5]] enzymes actually are [[GH30] enzymes.
+The family classification of a number of [[GH30]] members was revised in 2010 <cite>stjohn2010</cite>. In several studies concerning glucuronoxylan xylanohydrolases previously classified into [[GH5]], sequence analysis had suggested that these enzymes were more closely related to [[GH30]] members <cite>brumshtein2006,haegeman2009,keen1996,larson2003, mitreva-dautova2006</cite>.  In consideration of these observations, the revised classification of St. John ''et al.'' employed phylogenetics, primary amino acid sequence and tertiary structure analysis to show that the glucuronoxylan xylanohydrolases in question, as well as several other enzyme groups previously classified as [[GH5]] members, were indeed better placed in [[GH30]] <cite>stjohn2010</cite>.
 ==Substrate Specificities==

@@ Line 27: / Line 27: @@
 ==Family Classification==
-[[GH30]] classification has recently been revised <cite>stjohn2010</cite>. It has been suggested previously is several reports that with respect to [[GH5]] glucuronoxylan xylanohydrolases
+[[GH30]] classification has recently been revised <cite>stjohn2010</cite>. As had been suggested in several reports with respect to glucuronoxylan xylanohydrolases (previously of [[GH5]])<cite>brumshtein2006,haegeman2009,keen1996,larson2003, mitreva-dautova2006</cite>, these enzymes through sequence analysis appear to be more like enzymes of [[GH30]].
 ==Substrate Specificities==
@@ Line 50: / Line 50: @@
 ==References==
 <biblio>
 # stjohn2010 pmid=20932833
 # grabowski2008 pmid=19094956

@@ Line 26: / Line 26: @@
 </div>
-==Substrate specificities==
+==Family Classification==
 This family contains [[glycoside hydrolases]] with three known enzyme activities: &beta;-glucosylceramidase, &beta;-1,6-glucanase, and &beta;-xylosidase. This family currently contains enzymes from only bacteria and eukaryotes. The best-studied enzyme is human &beta;-glucocerebrosidase whose deficiency causes Gauchers disease <cite>grabowski2008</cite>. This enzyme is responsible for hydrolyzing the &beta;-glucoside from the glycolipid glucosylceramide.
@@ Line 35: / Line 38: @@
 The [[catalytic nucleophile]] was first identified in human &beta;-glucocerebrosidase as Glu340 in the sequence FAS<u>'''E'''</u>A by trapping of the 2-deoxy-2-fluoro-glucosyl-enzyme [[intermediate]] and subsequent peptide mapping by LC/MS-MS <cite>miao1994</cite>. The [[catalytic nucleophile]] had been previously been mistakenly identified as Asp443 using a tritiated bromoconduritol epoxide <cite>dinur1986, legler1990</cite>, although subsequent kinetic analyses of site-directed mutants of Asp443 were not consistent with its role as the [[catalytic nucleophile]] <cite>grace1994</cite>. The [[general acid/base]] residue of human &beta;-glucoerebrosidase is predicted to be Glu-274 <cite>durand1997</cite>. While this identification has not been experimentally verified through analysis of variant proteins created by mutation of that site, it is consistent with structural studies (below).
-==Three-dimensional structures==
+==Three-Dimensional Structures==
 The three-dimensional structure of human &beta;-glucocerebrosidase was first solved in 2003 <cite>dvir2003</cite>, and since then several different structures of this enzyme have been reported (reviewed in <cite>kacher2008</cite>). GH30 enzymes are members of the GHA clan fold, consistent with the classic (&alpha;/&beta;)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids located at the C-terminal ends of &beta;-strands 4 (acid/base) and 7 (nucleophile) <cite>henrissat1995</cite>.
@@ Line 47: / Line 50: @@
 ==References==
 <biblio>
 # grabowski2008 pmid=19094956
 # grabowski1990 pmid=2127241

@@ Line 27: / Line 27: @@
 ==Substrate specificities==
-This family contains [[glycoside hydrolases]] with three known enzyme activities: &beta;-glucosylceramidase, &beta;-1,6-glucanase, and &beta;-xylosidase. This family currently contains enzymes from only bacteria and eukaryotes. The best-studied enzyme is human &beta;-glucocerebrosidase whose deficiency causes Gauchers disease <cite>#1</cite>. This enzyme is responsible for hydrolyzing the &beta;-glucoside from the glycolipid glucosylceramide.
+This family contains [[glycoside hydrolases]] with three known enzyme activities: &beta;-glucosylceramidase, &beta;-1,6-glucanase, and &beta;-xylosidase. This family currently contains enzymes from only bacteria and eukaryotes. The best-studied enzyme is human &beta;-glucocerebrosidase whose deficiency causes Gauchers disease <cite>grabowski2008</cite>. This enzyme is responsible for hydrolyzing the &beta;-glucoside from the glycolipid glucosylceramide.
 ==Kinetics and Mechanism==
-Family GH30 enzymes are [[retaining]] enzymes. Although this has never been formally demonstrated experimentally through NMR analysis of the initially formed sugar product, covalent trapping of the [[catalytic nucleophile]] (described below) conclusively demonstrates that these enzymes follow the classic [[Koshland double-displacement mechanism]]. The &beta;-glucosylceramidases require an activator protein and negatively charged phospholipids for optimal activity, <cite>#2</cite> although the role of these activators is still not entirely clear. Neither the &beta;-1,6-glucanases <cite>#3</cite> nor the &beta;-xylosidases <cite>#4</cite> appear to require any activators.
+Family GH30 enzymes are [[retaining]] enzymes. Although this has never been formally demonstrated experimentally through NMR analysis of the initially formed sugar product, covalent trapping of the [[catalytic nucleophile]] (described below) conclusively demonstrates that these enzymes follow the classic [[Koshland double-displacement mechanism]]. The &beta;-glucosylceramidases require an activator protein and negatively charged phospholipids for optimal activity, <cite>grabowski1990</cite> although the role of these activators is still not entirely clear. Neither the &beta;-1,6-glucanases <cite>oyama2002</cite> nor the &beta;-xylosidases <cite>brunner2002</cite> appear to require any activators.
 ==Catalytic Residues==
-The [[catalytic nucleophile]] was first identified in human &beta;-glucocerebrosidase as Glu340 in the sequence FAS<u>'''E'''</u>A by trapping of the 2-deoxy-2-fluoro-glucosyl-enzyme [[intermediate]] and subsequent peptide mapping by LC/MS-MS <cite>#5</cite>. The [[catalytic nucleophile]] had been previously been mistakenly identified as Asp443 using a tritiated bromoconduritol epoxide <cite>#6 #7</cite>, although subsequent kinetic analyses of site-directed mutants of Asp443 were not consistent with its role as the [[catalytic nucleophile]] <cite>#8</cite>. The [[general acid/base]] residue of human &beta;-glucoerebrosidase is predicted to be Glu-274 <cite>#9</cite>. While this identification has not been experimentally verified through analysis of variant proteins created by mutation of that site, it is consistent with structural studies (below).
+The [[catalytic nucleophile]] was first identified in human &beta;-glucocerebrosidase as Glu340 in the sequence FAS<u>'''E'''</u>A by trapping of the 2-deoxy-2-fluoro-glucosyl-enzyme [[intermediate]] and subsequent peptide mapping by LC/MS-MS <cite>miao1994</cite>. The [[catalytic nucleophile]] had been previously been mistakenly identified as Asp443 using a tritiated bromoconduritol epoxide <cite>dinur1986, legler1990</cite>, although subsequent kinetic analyses of site-directed mutants of Asp443 were not consistent with its role as the [[catalytic nucleophile]] <cite>grace1994</cite>. The [[general acid/base]] residue of human &beta;-glucoerebrosidase is predicted to be Glu-274 <cite>durand1997</cite>. While this identification has not been experimentally verified through analysis of variant proteins created by mutation of that site, it is consistent with structural studies (below).
 ==Three-dimensional structures==
-The three-dimensional structure of human &beta;-glucocerebrosidase was first solved in 2003 <cite>#10</cite>, and since then several different structures of this enzyme have been reported (reviewed in <cite>#11</cite>). GH30 enzymes are members of the GHA clan fold, consistent with the classic (&alpha;/&beta;)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids located at the C-terminal ends of &beta;-strands 4 (acid/base) and 7 (nucleophile) <cite>#12</cite>.
+The three-dimensional structure of human &beta;-glucocerebrosidase was first solved in 2003 <cite>dvir2003</cite>, and since then several different structures of this enzyme have been reported (reviewed in <cite>kacher2008</cite>). GH30 enzymes are members of the GHA clan fold, consistent with the classic (&alpha;/&beta;)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids located at the C-terminal ends of &beta;-strands 4 (acid/base) and 7 (nucleophile) <cite>henrissat1995</cite>.
 ==Family Firsts==
@@ Line 47: / Line 47: @@
 ==References==
 <biblio>
-#1 pmid=19094956
+# grabowski2008 pmid=19094956
-#2 pmid=2127241
+# grabowski1990 pmid=2127241
-#3 pmid=12162562
+# oyama2002 pmid=12162562
-#4 pmid=11909624
+# brunner2002 pmid=11909624
-#5 pmid=7908905
+# miao1994 pmid=7908905
-#6 pmid=3456607
+# dinur1986 pmid=3456607
-#7 pmid=2077872
+# legler1990 pmid=2077872
-#8 pmid=8294487
+# grace1994 pmid=8294487
-#9 pmid=9134434
+# durand1997 pmid=9134434
-#10 pmid=12792654
+# dvir2003 pmid=12792654
-#11 pmid=18783340
+# kacher2008 pmid=18783340
-#12 pmid=7624375
+# henrissat1995 pmid=7624375
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH030]]