Glycoside Hydrolase Family 9 - Revision history

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

2021-12-18T21:18:23Z

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

Harry Brumer at 17:32, 4 April 2019

2019-04-04T17:32:17Z

Harry Brumer at 17:31, 4 April 2019

2019-04-04T17:31:36Z

Harry Brumer at 17:23, 4 April 2019

2019-04-04T17:23:56Z

Harry Brumer: Add xyloglucanase info references

2019-04-04T17:16:45Z

Add xyloglucanase info references

Harry Brumer at 17:06, 10 October 2016

2016-10-10T17:06:41Z

Harry Brumer at 00:24, 8 October 2016

2016-10-08T00:24:30Z

Harry Brumer at 16:12, 29 July 2015

2015-07-29T16:12:51Z

Breeanna Urbanowicz at 17:24, 9 March 2015

2015-03-09T17:24:41Z

Spencer Williams at 06:28, 29 August 2010

2010-08-29T06:28:45Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]s: ^^^David Wilson^^^ and ^^^Breeanna Urbanowicz^^^
+* [[Author]]s: [[User:David Wilson|David Wilson]] and [[User:Breeanna Urbanowicz|Breeanna Urbanowicz]]
-* [[Responsible Curator]]:  ^^^David Wilson^^^
+* [[Responsible Curator]]:  [[User:David Wilson|David Wilson]]
 ----

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-Members of family GH9 are mainly cellulases ([{{EClink}}3.2.1.4 EC 3.2.1.4]), including primarily endo-glucanases and a few processive endo-glucanases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  More recently, certain GH9 members from ''Clostridia'' <cite>Ravachol2016</cite> and ''Bacteroides'' <cite>Larsbrink2014 Foley2019</cite> have been shown to be endo-xyloglucanases ([{{EClink}}3.2.1.151 EC 3.2.1.151]) or mixed-linkage endo-glucanases ([{{EClink}}3.2.1.73 EC 3.2.1.73]).  Exo-beta-glucosaminidases are also found in this family <cite>Honda2016 Wu2018</cite>.
+Members of family GH9 are mainly cellulases ([{{EClink}}3.2.1.4 EC 3.2.1.4]), including primarily endo-glucanases and a few processive endo-glucanases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  More recently, certain GH9 members from ''Clostridia'' <cite>Ravachol2016</cite> and ''Bacteroides'' <cite>Larsbrink2014 Foley2019</cite> have been shown to be endo-xyloglucanases ([{{EClink}}3.2.1.151 EC 3.2.1.151]) or mixed-linkage endo-glucanases ([{{EClink}}3.2.1.73 EC 3.2.1.73]).  Exo-beta-glucosaminidases ([{{EClink}}3.2.1.165 EC 3.2.1.165]) are also found in this family <cite>Honda2016 Wu2018</cite>.
 All of the processive endoglucanases contain a family 3c CBM rigidly attached to the C-terminus of the GH9 catalytic domain (cd) <cite>Sakon1997</cite>. This domain is part of the active site and is essential for processivity <cite>Sakon1997</cite>.  [[CBM3]]c domains bind weakly to cellulose as they lack several of the conserved aromatic residues that are important for cellulose binding in family 3a and family 3b members <cite>Tormo1996</cite>.  All known plant cellulases belong to GH9, and most of the other members are eubacterial although there are two archael members and some fungal, earthworm,  arthropod, chordate, echinoderma and molusk members. There are two subgroups in GH9, E1 which contains only cellulases from bacteria, including ones from both aerobes and anaeobes, and E2 which includes some bacterial and all nonbacterial cellulases <cite>Tomme1995</cite>. An evolutionary study shows that the eucaryote members contain two monophyletic groups that are ancient; one including all animal members and the other including all plant members <cite>Davison2005</cite>. All known processive endoglucanase genes are in subgroup E1.

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-Members of family GH9 are mainly cellulases ([{{EClink}}3.2.1.4 EC 3.2.1.4]), including primarily endo-glucanases and a few processive endo-glucanases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  More recently, certain GH9 members from ''Clostridia'' <cite>Ravachol2016</cite> and ''Bacteroides'' <cite>Larsbrink2014 Foley2019</cite> have been shown to be endo-xyloglucanases ([{{EClink}}3.2.1.151 EC 3.2.1.151]) or mixed-linkage endo-glucanases ([{{EClink}}3.2.1.73 EC 3.2.1.73]).
+Members of family GH9 are mainly cellulases ([{{EClink}}3.2.1.4 EC 3.2.1.4]), including primarily endo-glucanases and a few processive endo-glucanases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  More recently, certain GH9 members from ''Clostridia'' <cite>Ravachol2016</cite> and ''Bacteroides'' <cite>Larsbrink2014 Foley2019</cite> have been shown to be endo-xyloglucanases ([{{EClink}}3.2.1.151 EC 3.2.1.151]) or mixed-linkage endo-glucanases ([{{EClink}}3.2.1.73 EC 3.2.1.73]).  Exo-beta-glucosaminidases are also found in this family <cite>Honda2016 Wu2018</cite>.
 All of the processive endoglucanases contain a family 3c CBM rigidly attached to the C-terminus of the GH9 catalytic domain (cd) <cite>Sakon1997</cite>. This domain is part of the active site and is essential for processivity <cite>Sakon1997</cite>.  [[CBM3]]c domains bind weakly to cellulose as they lack several of the conserved aromatic residues that are important for cellulose binding in family 3a and family 3b members <cite>Tormo1996</cite>.  All known plant cellulases belong to GH9, and most of the other members are eubacterial although there are two archael members and some fungal, earthworm,  arthropod, chordate, echinoderma and molusk members. There are two subgroups in GH9, E1 which contains only cellulases from bacteria, including ones from both aerobes and anaeobes, and E2 which includes some bacterial and all nonbacterial cellulases <cite>Tomme1995</cite>. An evolutionary study shows that the eucaryote members contain two monophyletic groups that are ancient; one including all animal members and the other including all plant members <cite>Davison2005</cite>. All known processive endoglucanase genes are in subgroup E1.
@@ Line 76: / Line 76: @@
 #Larsbrink2014 pmid=24463512
 #Ravachol2016 pmid=26946939
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH009]]

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-Members of family GH9 are mainly cellulases (EC 3.2.1.4), including primarily endo-glucanases and a few processive endo-glucanases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  More recently, certain GH9 members from ''Clostridia'' <cite>Ravachol2016</cite> and ''Bacteroides'' <cite>Foley2019</cite> have been shown to be endo-xyloglucanases (EC 3.2.1.151).
+Members of family GH9 are mainly cellulases ([{{EClink}}3.2.1.4 EC 3.2.1.4]), including primarily endo-glucanases and a few processive endo-glucanases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  More recently, certain GH9 members from ''Clostridia'' <cite>Ravachol2016</cite> and ''Bacteroides'' <cite>Larsbrink2014 Foley2019</cite> have been shown to be endo-xyloglucanases ([{{EClink}}3.2.1.151 EC 3.2.1.151]) or mixed-linkage endo-glucanases ([{{EClink}}3.2.1.73 EC 3.2.1.73]).
 All of the processive endoglucanases contain a family 3c CBM rigidly attached to the C-terminus of the GH9 catalytic domain (cd) <cite>Sakon1997</cite>. This domain is part of the active site and is essential for processivity <cite>Sakon1997</cite>.  [[CBM3]]c domains bind weakly to cellulose as they lack several of the conserved aromatic residues that are important for cellulose binding in family 3a and family 3b members <cite>Tormo1996</cite>.  All known plant cellulases belong to GH9, and most of the other members are eubacterial although there are two archael members and some fungal, earthworm,  arthropod, chordate, echinoderma and molusk members. There are two subgroups in GH9, E1 which contains only cellulases from bacteria, including ones from both aerobes and anaeobes, and E2 which includes some bacterial and all nonbacterial cellulases <cite>Tomme1995</cite>. An evolutionary study shows that the eucaryote members contain two monophyletic groups that are ancient; one including all animal members and the other including all plant members <cite>Davison2005</cite>. All known processive endoglucanase genes are in subgroup E1.
@@ Line 40: / Line 40: @@
 == Three-dimensional structures ==
-All reported GH9 catalytic domain structures have an (a/a)<sub>6</sub> barrel fold that contains an open active site cleft that contains at least six sugar binding subsites -4 to +2 <cite>Sakon1997 Geurin2002</cite>. In processive endoglucanases the catalytic domain is joined to a family 3c carbohydrate-binding module that is aligned with the active site cleft <cite>Sakon1997</cite>.
+All reported GH9 catalytic domain structures have an (a/a)<sub>6</sub> barrel fold that contains an open active site cleft that contains at least six sugar binding subsites -4 to +2 <cite>Sakon1997 Geurin2002 Foley2019</cite>. In processive endoglucanases the catalytic domain is joined to a family 3c carbohydrate-binding module that is aligned with the active site cleft <cite>Sakon1997</cite>.
 == Family Firsts ==
@@ Line 73: / Line 73: @@
 #Gilkes1991 pmid=1886523
 #Chavaux1992 pmid=1537833
 #Foley2019 pmid=30668971
+#Larsbrink2014 pmid=24463512
 #Ravachol2016 pmid=26946939
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH009]]

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family GH9 are mainly cellulases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  GH9 is the second largest cellulase family. It contains mainly endoglucanases with a few processive endoglucanases. All of the processive endoglucanases contain a family 3c CBM rigidly attached to the C-terminus of the GH9 catalytic domain (cd) <cite>Sakon1997</cite>. This domain is part of the active site and is essential for processivity <cite>Sakon1997</cite>.  CBM3c domains bind weakly to cellulose as they lack several of the conserved aromatic residues that are important for cellulose binding in family 3a and family 3b members <cite>Tormo1996</cite>.  All known plant cellulases belong to GH9, and most of the other members are eubacterial although there are two archael members and some fungal, earthworm,  arthropod, chordate, echinoderma and molusk members. There are two subgroups in GH9, E1 which contains only cellulases from bacteria, including ones from both aerobes and anaeobes, and E2 which includes some bacterial and all nonbacterial cellulases <cite>Tomme1995</cite>. An evolutionary study shows that the eucaryote members contain two monophyletic groups that are ancient; one including all animal members and the other including all plant members <cite>Davison2005</cite>. All known processive endoglucanase genes are in subgroup E1.
+Members of family GH9 are mainly cellulases (EC 3.2.1.4), including primarily endo-glucanases and a few processive endo-glucanases.  Indeed, as one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, GH9 was previously known as "Cellulase Family E" <cite>Henrissat1989 Gilkes1991</cite>.  More recently, certain GH9 members from ''Clostridia'' <cite>Ravachol2016</cite> and ''Bacteroides'' <cite>Foley2019</cite> have been shown to be endo-xyloglucanases (EC 3.2.1.151).
 Most plant GH9 enzymes studied to date are endoglucanases ("cellulases", EC [{{EClink}}3.2.1.4 3.2.1.4]) with little or no activity on crystalline cellulose, but with discernible activity on soluble cellulose derivatives, including carboxymethyl cellulose (CMC), phosphoric acid swollen non-crystalline cellulose, and numerous plant polysaccharides including xylan, 1,3-1,4-ß-glucan, xyloglucan, and glucomannan <cite>Master2004 YoshidaKomae2006 Ohmiya2000 Woolley2001 Urbanowicz2007</cite>.  Due to their ubiquity and large numbers, the phylogeny of plant GH9 enzymes has been further sub-divided into three classes <cite>UrbanowiczBennett2007</cite>, which are described in detail on the [[Glycoside_Hydrolase_Family_9/Plant_endoglucanases|plant GH9 endoglucanase subpage]].
@@ Line 72: / Line 73: @@
 #Gilkes1991 pmid=1886523
 #Chavaux1992 pmid=1537833
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH009]]

@@ Line 11: / Line 11: @@
 |-
 |'''Clan'''
-|GH-G
+|not assigned
 |-
 |'''Mechanism'''

@@ Line 46: / Line 46: @@
 ;First [[general base]] identification: Asp 58 in ''T. fusca'' Cel9A was shown to be the [[general base]] by site directed mutagenesis and azide rescue <cite>Li2007</cite>.
-;First [[general acid]] residue identification: Glu555 was shown to be the catalytic acid in ''C. thermocellum'' CelD by site directed mutagenesis <cite>Chavaux1962</cite>.
+;First [[general acid]] residue identification: Glu555 was shown to be the catalytic acid in ''C. thermocellum'' CelD by site directed mutagenesis <cite>Chavaux1992</cite>.
 ;First 3-D structure: The structure of endocellulase CelD from ''Clostridium thermocellum'' was determined by X-ray crystallography (PDB ID [{{PDBlink}}1clc 1clc]) <cite>Lascombe1995</cite>.
@@ Line 71: / Line 71: @@
 #Henrissat1989 pmid=2806912
 #Gilkes1991 pmid=1886523
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH009]]