Glycoside Hydrolase Family 6 - Revision history

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

2021-12-18T21:15:33Z

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

Kazune Tamura: /* Three-dimensional structures */

2019-02-23T23:26:22Z

Three-dimensional structures

Harry Brumer at 16:09, 29 July 2015

2015-07-29T16:09:05Z

Harry Brumer: updated CAZyDBlink

2012-09-10T16:31:18Z

updated CAZyDBlink

Spencer Williams at 01:40, 9 June 2011

2011-06-09T01:40:38Z

Gideon Davies at 12:35, 3 December 2010

2010-12-03T12:35:26Z

Spencer Williams at 10:18, 13 October 2010

2010-10-13T10:18:40Z

Gideon Davies at 14:49, 11 October 2010

2010-10-11T14:49:38Z

Harry Brumer: /* Family Firsts */

2010-10-06T09:59:17Z

Family Firsts

Gideon Davies at 09:48, 6 October 2010

2010-10-06T09:48:00Z

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 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Kathleen Piens^^^ and ^^^Gideon Davies^^^
+* [[Author]]: [[User:Kathleen Piens|Kathleen Piens]] and [[User:Gideon Davies|Gideon Davies]]
-* [[Responsible Curator]]:  ^^^Gideon Davies^^^
+* [[Responsible Curator]]:  [[User:Gideon Davies|Gideon Davies]]
 ----

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 The first crystal structures of cellobiohydrolases and endoglucanases from family [[GH6]] revealed modified &alpha;/&beta; barrel folds which, unlike the classical (&beta;/&alpha;)<sub>8</sub> "TIM" barrel has just seven &beta;-strands forming the central &beta;-barrel. The CBHII structure revealed an active centre (see above) enclosed in a tunnel formed primarily by two surface loops. When, subsequently, the first endoglucanase from GH6 was solved, the active center was observed in a long open groove. The comparison of these two structures thus provided the first insight into how endo or processive activity was modulated, through display of the active centre in a in an open grove, or loop-enclosed tunnel, respectively. In 1995 the UBC group were able to truncate the extended loops of a cellobiohydrolase resulting in an enzyme with more endo-activity <cite>Meinke1995</cite>.  To this day the debate continues about the possibilities of loop conformational change in moderating the activity of cellobiohydrolases between exo and endo. Ståhlberg was perhaps the first to explicitly state that ''T. reesei'' "has no true exo-cellulases" <cite>Stberg1993</cite>. It is clear that there is no absolute steric demand for the ''exo'' activity of cellobiohydrolases; the enzymes have a viable "-3" subsite <cite>Varrot1999, Varrot2003</cite>, the loops of the cellobiohydrolases are clearly mobile and show multiple conformations (consistent with occasional opening to support ''endo''-activity, and are also able to act on artificial substrates in which both ends have large appended groups (for example <cite>Armand1997</cite>).
-The nature of how catalysis was achived, and the conformational itinerary of catalysis was first provided by the Uppsala, Grenoble and Gent groups in 1999 <cite>Zou1999</cite> was a trapped Michaelis complex of a thio-oligosaccharide was observed spanning the active centre with the -1 subsite sugar in <sup>2</sup>''S''<sub>O</sub> conformation, which suggested a pathway around the <sup>2,5</sup>''B'' [[transition state]] conformation. Subsequent structural <cite>Varrot2005 Varrot2002</cite> and modelling <cite>Koivula2002</cite> support for these proposals comes from similarly distorted species on other GH6 enzymes and from the observation of a "cellobiosyl isofagomine" in <sup>2,5</sup>''B'' conformation <cite>Varrot2003</cite>.
+The nature of how catalysis was achieved, and the conformational itinerary of catalysis was first provided by the Uppsala, Grenoble and Gent groups in 1999 <cite>Zou1999</cite> was a trapped Michaelis complex of a thio-oligosaccharide was observed spanning the active centre with the -1 subsite sugar in <sup>2</sup>''S''<sub>O</sub> conformation, which suggested a pathway around the <sup>2,5</sup>''B'' [[transition state]] conformation. Subsequent structural <cite>Varrot2005 Varrot2002</cite> and modelling <cite>Koivula2002</cite> support for these proposals comes from similarly distorted species on other GH6 enzymes and from the observation of a "cellobiosyl isofagomine" in <sup>2,5</sup>''B'' conformation <cite>Varrot2003</cite>.
 == Family Firsts ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family GH6 cleave &beta;-1,4 glycosidic bonds in cellulose / &beta;-1,4-glucans. Only endoglucanase (EC [{{EClink}}3.2.1.4 3.2.1.4]) and cellobiohydrolase (EC [{{EClink}}3.2.1.91 3.2.1.91]) activity has been reported for the bacterial and eukaryotic members of this family.
+[[Glycoside hydrolases]] of family GH6 cleave &beta;-1,4 glycosidic bonds in cellulose / &beta;-1,4-glucans. Only endoglucanase (EC [{{EClink}}3.2.1.4 3.2.1.4]) and cellobiohydrolase (EC [{{EClink}}3.2.1.91 3.2.1.91]) activity has been reported for the bacterial and eukaryotic members of this family. GH6 was one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, and was previously known as "Cellulase Family B" <cite>Henrissat1989 Gilkes1991</cite>.
 == Kinetics and Mechanism ==
@@ Line 112: / Line 112: @@
 #Armand1997 pmid=9006908
 #Stberg1993 pmid=8499476
+#Henrissat1989 pmid=2806912
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH006]]

@@ Line 22: / Line 22: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH6.html
+| colspan="2" |{{CAZyDBlink}}GH6.html
 |}
 </div>

@@ Line 31: / Line 31: @@
 == Kinetics and Mechanism ==
-GH6 enzymes perform catalysis with [[inverting|inversion]] of anomeric stereochemistry, as first shown by NMR <cite>Knowles1988</cite> on Cellobiohydrolase II (CBH II; Cel6A) from the fungus ''Trichoderma reesei'' (a clonal derivative of ''Hypocrea jecorina'' <cite>Kuhls1996</cite>).
+GH6 enzymes perform catalysis with [[inverting|inversion]] of anomeric stereochemistry, as first shown by NMR <cite>Knowles1988</cite> on cellobiohydrolase II (CBH II; Cel6A) from the fungus ''Trichoderma reesei'' (a clonal derivative of ''Hypocrea jecorina'' <cite>Kuhls1996</cite>).
 == Catalytic Residues ==
-The first 3-D structure of CBHII provided a strong clue as to the identification of the catalytic [[general acid]] in the [[inverting]] mechanism (Asp 221 in the case of this ''Trichoderma reesei'' Cel6A enzyme). This assigment has withstood the tests of time with strong kinetic support (from kinetics as a function of leaving group ability for a series of enzyme variants) <cite>Damude1995</cite> as well as from all subsequent 3-D analyses of enzyme-ligand complexes (for example <cite>Zou1999 Varrot2005 Varrot2002</cite> ). The identification of the catalytic [[general base]] is, however, far less clear. Simply put this is because there is no clear potential base within hydrogen-bonding distance of a water molecule that could act as the nucleophile in the [[inverting]] mechanism. Thus, although there are mutagenesis / kinetic proposals for a base <cite>Damude1995</cite>, the current 'Zeitgeist' is that the attacking water is deprotonated via a string of water molecules in what Sinnott has descibed as a "Grotthuss" mechanism; for which there is solvent kinetic isotope effect support <cite>Koivula2002</cite>. On the basis of structure the residue most likely to act as the [[general base]] is Asp175 on the ''Trichoderma reesei'' Cel6A, although Asp401 may also play a role (see Table 1).
+The first 3D structure of CBHII provided a strong clue as to the identification of the catalytic [[general acid]] in the [[inverting]] mechanism (Asp 221 in the case of this ''Trichoderma reesei'' Cel6A enzyme). This assigment has withstood the tests of time with strong kinetic support (from kinetics as a function of leaving group ability for a series of enzyme variants) <cite>Damude1995</cite> as well as from all subsequent 3-D analyses of enzyme-ligand complexes (for example <cite>Zou1999 Varrot2005 Varrot2002</cite> ). The identification of the catalytic [[general base]] is, however, far less clear. Simply put this is because there is no clear potential base within hydrogen-bonding distance of a water molecule that could act as the nucleophile in the [[inverting]] mechanism. Thus, although there are mutagenesis / kinetic proposals for a base <cite>Damude1995</cite>, the current 'Zeitgeist' is that the attacking water is deprotonated via a string of water molecules in what Sinnott has descibed as a "Grotthuss" mechanism; for which there is solvent kinetic isotope effect support <cite>Koivula2002</cite>. On the basis of structure the residue most likely to act as the [[general base]] is Asp175 on the ''Trichoderma reesei'' Cel6A, although Asp401 may also play a role (see Table 1).

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 6 cleave &beta;-1,4 glycosidic bonds in cellulose / &beta;-1,4-glucans. Only endoglucanase (EC [{{EClink}}3.2.1.4 3.2.1.4]) and cellobiohydrolase (EC [{{EClink}}3.2.1.91 3.2.1.91]) activity has been reported for both bacterial and eukaryotic members of this family.
+[[Glycoside hydrolases]] of family GH6 cleave &beta;-1,4 glycosidic bonds in cellulose / &beta;-1,4-glucans. Only endoglucanase (EC [{{EClink}}3.2.1.4 3.2.1.4]) and cellobiohydrolase (EC [{{EClink}}3.2.1.91 3.2.1.91]) activity has been reported for the bacterial and eukaryotic members of this family.
 == Kinetics and Mechanism ==
-Family 6 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Knowles1988</cite> on Cellobiohydrolase II (CBH II; Cel6A) from the fungus ''Trichoderma reesei'' (a clonal derivative of ''Hypocrea jecorina'' <cite>Kuhls1996</cite>).
+GH66 enzymes perform catalysis with [[inverting|inversion]] of anomeric stereochemistry, as first shown by NMR <cite>Knowles1988</cite> on Cellobiohydrolase II (CBH II; Cel6A) from the fungus ''Trichoderma reesei'' (a clonal derivative of ''Hypocrea jecorina'' <cite>Kuhls1996</cite>).
 == Catalytic Residues ==
-The first 3-D structure of CBHII provided a strong clue as to the identification of the catalytic acid in the inverting mechanism (Asp 221 in the case of this ''Trichoderma reesei'' Cel6A enzyme. This assigment has withstood the tests of time with strong kinetic support (from kinetics as a function of leaving group ability for a series of enzyme variants) <cite>Damude1995</cite> as well as from all subsequent 3-D analyses of enzyme-ligand complexes (for example <cite>Zou1999 Varrot2005 Varrot2002</cite> ). The identification of the base is, however, far less clear. Simply put this is because there is no clear potential base within hydrogen-bonding distance of a water molecule that could act as the nucleophile in the inversion mechanism. Thus, although there are mutagenesis / kinetic proposals for a base <cite>Damude1995</cite>, the current Zeitgeist is that the attacking water is deprotonated via a string of water molecules in what Sinnott has descibed as a "Grotthuss" mechanism; for which there is solvent kinetic isotope effect support <cite>Koivula2002</cite>. On the basis of structure the residue most likely to act as the base is Asp175 on the ''Trichoderma reesei'' Cel6A although Asp401 may also play a role (see Table 1).
+The first 3-D structure of CBHII provided a strong clue as to the identification of the catalytic [[general acid]] in the [[inverting]] mechanism (Asp 221 in the case of this ''Trichoderma reesei'' Cel6A enzyme). This assigment has withstood the tests of time with strong kinetic support (from kinetics as a function of leaving group ability for a series of enzyme variants) <cite>Damude1995</cite> as well as from all subsequent 3-D analyses of enzyme-ligand complexes (for example <cite>Zou1999 Varrot2005 Varrot2002</cite> ). The identification of the catalytic [[general base]] is, however, far less clear. Simply put this is because there is no clear potential base within hydrogen-bonding distance of a water molecule that could act as the nucleophile in the [[inverting]] mechanism. Thus, although there are mutagenesis / kinetic proposals for a base <cite>Damude1995</cite>, the current 'Zeitgeist' is that the attacking water is deprotonated via a string of water molecules in what Sinnott has descibed as a "Grotthuss" mechanism; for which there is solvent kinetic isotope effect support <cite>Koivula2002</cite>. On the basis of structure the residue most likely to act as the [[general base]] is Asp175 on the ''Trichoderma reesei'' Cel6A, although Asp401 may also play a role (see Table 1).
@@ Line 83: / Line 83: @@
 |}
 ----
@@ Line 89: / Line 88: @@
 The first crystal structures of cellobiohydrolases and endoglucanases from family [[GH6]] revealed modified &alpha;/&beta; barrel folds which, unlike the classical (&beta;/&alpha;)<sub>8</sub> "TIM" barrel has just seven &beta;-strands forming the central &beta;-barrel. The CBHII structure revealed an active centre (see above) enclosed in a tunnel formed primarily by two surface loops. When, subsequently, the first endoglucanase from GH6 was solved, the active center was observed in a long open groove. The comparison of these two structures thus provided the first insight into how endo or processive activity was modulated, through display of the active centre in a in an open grove, or loop-enclosed tunnel, respectively. In 1995 the UBC group were able to truncate the extended loops of a cellobiohydrolase resulting in an enzyme with more endo-activity <cite>Meinke1995</cite>.  To this day the debate continues about the possibilities of loop conformational change in moderating the activity of cellobiohydrolases between exo and endo. Ståhlberg was perhaps the first to explicitly state that ''T. reesei'' "has no true exo-cellulases" <cite>Stberg1993</cite>. It is clear that there is no absolute steric demand for the ''exo'' activity of cellobiohydrolases; the enzymes have a viable "-3" subsite <cite>Varrot1999, Varrot2003</cite>, the loops of the cellobiohydrolases are clearly mobile and show multiple conformations (consistent with occasional opening to support ''endo''-activity, and are also able to act on artificial substrates in which both ends have large appended groups (for example <cite>Armand1997</cite>).
-The nature of how catalysis was achived, and the conformational itinerary of catalysis was first provided by the Uppsala, Grenoble and Gent groups in 1999 <cite>Zou1999</cite> was a trapped Michaelis complex of a thio-oligosaccharide was observed spanning the active centre with the -1 subsite sugar in <sup>2</sup>S<sub>O</sub> conformation which suggestad a pathway around the <sup>2,5</sup>B conformation. Subsequent structural <cite>Varrot2005 Varrot2002</cite> and modelling <cite>Koivula2002</cite> support for these proposals comes from similarly distorted species on other GH6 enzymes and from the observation of a "cellobiosyl isofagomine" in <sup>2,5</sup>B conformation <cite>Varrot2003</cite>.
+The nature of how catalysis was achived, and the conformational itinerary of catalysis was first provided by the Uppsala, Grenoble and Gent groups in 1999 <cite>Zou1999</cite> was a trapped Michaelis complex of a thio-oligosaccharide was observed spanning the active centre with the -1 subsite sugar in <sup>2</sup>''S''<sub>O</sub> conformation, which suggested a pathway around the <sup>2,5</sup>''B'' [[transition state]] conformation. Subsequent structural <cite>Varrot2005 Varrot2002</cite> and modelling <cite>Koivula2002</cite> support for these proposals comes from similarly distorted species on other GH6 enzymes and from the observation of a "cellobiosyl isofagomine" in <sup>2,5</sup>''B'' conformation <cite>Varrot2003</cite>.
 == Family Firsts ==
 ;First sterochemistry determination: ''Hypocrea jecorina'' cellobiohydrolase Cel6A by NMR <cite>Knowles1988</cite>.
-;First general acid/base residue identification: The role of Asp221 as the potential caralytic acid was first proposed on the basis of 3-D structure of the ''Hypocrea jecorina'' cellobiohydrolase CBHII / Cel6A <cite>Rouvinen1990</cite>. Enzyme kinetics of variants, in conjunction with leaving groups requiring provided strong confirmation <cite>Damude1995</cite>. The existance / identification of the base is less clear and current beliefs are that the water is deprotonated via a "solvent wire" through to one of the conserved aspratates near the active centre.
+;First [[general acid]] residue identification: The role of Asp221 as the potential catalytic acid was first proposed on the basis of 3-D structure of the ''Hypocrea jecorina'' cellobiohydrolase CBHII / Cel6A <cite>Rouvinen1990</cite>. Enzyme kinetics of variants, in conjunction with leaving groups requiring provided strong confirmation <cite>Damude1995</cite>.
+;First [[general base]] residue identification: The existence / identification of the catalytic base is less clear and current beliefs are that the water is deprotonated through a "solvent wire" through to one of the conserved aspartates near the active centre.
 ;First 3-D structure: The catalytic core domain of the ''Trichoderma reesei'' (the organism now known as ''Hypocrea jecorina'') cellobiohydrolase II by the Jones group <cite>Rouvinen1990</cite>.  The first endoglucanase in this family was the ''Thermomonospora fusca'' E2 enzyme (catalytic core) solved by the Wilson/Karplus groups<cite>Spezio1993</cite>

@@ Line 87: / Line 87: @@
 == Three-dimensional structures ==
-The first crystal structures of cellobiohydrolases and endoglucanases from family [[GH6]] revealed modified &alpha;/&beta; barrel folds which, unlike the classical (&beta;/&alpha;)<sub>8</sub> "TIM" barrel has just seven &beta;-strands forming the central &beta;-barrel. The CBHII structure revealed an active centre (see above) enclosed in a tunnel formed primarily by two surface loops. When, subsequently, the first endoglucanase from GH6 was solved, the active center was observed in a long open groove. The comparison of these two structures thus provided the first insight into how endo or processive activity was modulated, through display of the active centre in a in an open grove, or loop-enclosed tunnel, respectively. In 1995 the UBC group were able to truncate the extended loops of a cellobiohydrolase resulting in an enzyme with more endo-activity <cite>Meinke1995</cite>.  To this day the debate continues about the possibilities of loop conformational change in moderating the activity of cellobiohydrolases between exo and endo. Ståhlberg was perhaps the first to explicitly state that ''T. reesei'' "has no true exo-cellulases" <cite>Stberg1993</cite>. It is clear that there is no absolute steric demand for the ''exo'' activity of cellobiohydrolases; the enzymes have a viable "-3" subsite <cite>Varrot1999</cite><cite>Varrot2003</cite>, the loops of the cellobiohydrolases are clearly mobile and show multiple conformations (consistent with occasional opening to support ''endo''-activity, and are also able to act on artificial substrates in which both ends have large appended groups (for example <cite>Armand1997</cite>.
+The first crystal structures of cellobiohydrolases and endoglucanases from family [[GH6]] revealed modified &alpha;/&beta; barrel folds which, unlike the classical (&beta;/&alpha;)<sub>8</sub> "TIM" barrel has just seven &beta;-strands forming the central &beta;-barrel. The CBHII structure revealed an active centre (see above) enclosed in a tunnel formed primarily by two surface loops. When, subsequently, the first endoglucanase from GH6 was solved, the active center was observed in a long open groove. The comparison of these two structures thus provided the first insight into how endo or processive activity was modulated, through display of the active centre in a in an open grove, or loop-enclosed tunnel, respectively. In 1995 the UBC group were able to truncate the extended loops of a cellobiohydrolase resulting in an enzyme with more endo-activity <cite>Meinke1995</cite>.  To this day the debate continues about the possibilities of loop conformational change in moderating the activity of cellobiohydrolases between exo and endo. Ståhlberg was perhaps the first to explicitly state that ''T. reesei'' "has no true exo-cellulases" <cite>Stberg1993</cite>. It is clear that there is no absolute steric demand for the ''exo'' activity of cellobiohydrolases; the enzymes have a viable "-3" subsite <cite>Varrot1999, Varrot2003</cite>, the loops of the cellobiohydrolases are clearly mobile and show multiple conformations (consistent with occasional opening to support ''endo''-activity, and are also able to act on artificial substrates in which both ends have large appended groups (for example <cite>Armand1997</cite>).
 The nature of how catalysis was achived, and the conformational itinerary of catalysis was first provided by the Uppsala, Grenoble and Gent groups in 1999 <cite>Zou1999</cite> was a trapped Michaelis complex of a thio-oligosaccharide was observed spanning the active centre with the -1 subsite sugar in <sup>2</sup>S<sub>O</sub> conformation which suggestad a pathway around the <sup>2,5</sup>B conformation. Subsequent structural <cite>Varrot2005 Varrot2002</cite> and modelling <cite>Koivula2002</cite> support for these proposals comes from similarly distorted species on other GH6 enzymes and from the observation of a "cellobiosyl isofagomine" in <sup>2,5</sup>B conformation <cite>Varrot2003</cite>.