Glycoside Hydrolase Family 8 - Revision history

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

2021-12-18T21:15:56Z

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

Harry Brumer: /* Kinetics and Mechanism */

2020-08-19T00:28:57Z

Kinetics and Mechanism

Harry Brumer: Moved Glycosynthase subsection again, this time under Kinetics and Mechanism

2020-08-19T00:27:46Z

Moved Glycosynthase subsection again, this time under Kinetics and Mechanism

Harry Brumer: rearranged Subfamiles and Glycosynthase sections as subsections of standard GH page headings

2020-08-19T00:26:36Z

rearranged Subfamiles and Glycosynthase sections as subsections of standard GH page headings

Harry Brumer at 16:14, 29 July 2015

2015-07-29T16:14:52Z

Harry Brumer: /* Substrate specificities */

2011-05-27T11:15:24Z

Substrate specificities

Harry Brumer at 11:14, 27 May 2011

2011-05-27T11:14:48Z

Harry Brumer: updated reference identifiers to standard AuthorYear format to make future edting easier

2011-05-27T11:12:50Z

updated reference identifiers to standard AuthorYear format to make future edting easier

Spencer Williams at 11:44, 14 June 2010

2010-06-14T11:44:36Z

Shinya Fushinobu at 01:37, 25 November 2009

2009-11-25T01:37:46Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]s: ^^^Motomitsu Kitaoka^^^ and ^^^Shinya Fushinobu^^^
+* [[Author]]s: [[User:Motomitsu Kitaoka|Motomitsu Kitaoka]] and [[User:Shinya Fushinobu|Shinya Fushinobu]]
-* [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
+* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
 ----

@@ Line 28: / Line 28: @@
 == Kinetics and Mechanism ==
-Enzymes of glycoside hydrolase family 8 are [[inverting]] enzymes, as first shown by Fierobe ''et al.'' who monitored the reaction of endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) using proton NMR spectroscopy <CITE>Fierobe1993</CITE>. Hydrolysis by CelA is computationally simulated with QM/MM metadynamics <CITE>Petersen2009</CITE>.
+Enzymes of glycoside hydrolase family 8 are [[inverting]] enzymes, as first shown by Fierobe ''et al.'' who monitored the reaction of endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) using proton NMR spectroscopy <CITE>Fierobe1993</CITE>. Hydrolysis by CelA was computationally simulated with QM/MM metadynamics <CITE>Petersen2009</CITE>.
 === Glycosynthase engineering ===
 Reducing-end-xylose releasing exo-oligoxylanase from ''Bacillus halodurans'' C-125 is the first inverting GH that was converted to glycosynthase by mutating the general base residue <cite>Honda2006</cite>.

@@ Line 27: / Line 27: @@
 [[Glycoside hydrolases]] of family 8 cleave &beta;-1,4 linkages of &beta;-1,4 glucans, xylans (or xylooligosaccharides), chitosans, and lichenans (1,3-1,4-&beta;-D-glucan). All of GH8 members have been found from bacteria, and there are no members from Eukaryotic or Archaeal origin. The majority of the enzymes are [[endo]]-acting enzymes, but one member has an [[exo]]-activity that releases &beta;-D-xylose residues from the reducing end of xylooligosaccharides. The substrate specificities found in GH8 are: chitosanase (EC [{{EClink}}3.2.1.132 3.2.1.132]), cellulase (EC [{{EClink}}3.2.1.4 3.2.1.4]), licheninase (EC [{{EClink}}3.2.1.73 3.2.1.73]), endo-1,4-&beta;-xylanase (EC [{{EClink}}3.2.1.8 3.2.1.8]) and reducing-end-xylose releasing exo-oligoxylanase (EC [{{EClink}}3.2.1.156 3.2.1.156]).  GH8 was one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, and was previously known as "Cellulase Family D" <cite>Henrissat1989 Gilkes1991</cite>.
 === Glycosynthase engineering ===
 Reducing-end-xylose releasing exo-oligoxylanase from ''Bacillus halodurans'' C-125 is the first inverting GH that was converted to glycosynthase by mutating the general base residue <cite>Honda2006</cite>.
 == Catalytic Residues ==

@@ Line 26: / Line 26: @@
 == Substrate specificities ==
 [[Glycoside hydrolases]] of family 8 cleave &beta;-1,4 linkages of &beta;-1,4 glucans, xylans (or xylooligosaccharides), chitosans, and lichenans (1,3-1,4-&beta;-D-glucan). All of GH8 members have been found from bacteria, and there are no members from Eukaryotic or Archaeal origin. The majority of the enzymes are [[endo]]-acting enzymes, but one member has an [[exo]]-activity that releases &beta;-D-xylose residues from the reducing end of xylooligosaccharides. The substrate specificities found in GH8 are: chitosanase (EC [{{EClink}}3.2.1.132 3.2.1.132]), cellulase (EC [{{EClink}}3.2.1.4 3.2.1.4]), licheninase (EC [{{EClink}}3.2.1.73 3.2.1.73]), endo-1,4-&beta;-xylanase (EC [{{EClink}}3.2.1.8 3.2.1.8]) and reducing-end-xylose releasing exo-oligoxylanase (EC [{{EClink}}3.2.1.156 3.2.1.156]).  GH8 was one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, and was previously known as "Cellulase Family D" <cite>Henrissat1989 Gilkes1991</cite>.
 == Kinetics and Mechanism ==
@@ Line 35: / Line 38: @@
 The [[general base]] of GH8b subfamily was first identified in chitosanase from ''Bacillus'' sp. K17 as Glu309 based on its crystal structure and by making E309Q mutant <cite>Adachi2004</cite>.
-== Subfamilies ==
+== Three-dimensional structures ==
 GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base <cite>Adachi2004</cite>.
 GH8a has the general base (Asp) at the N-terminal end of &alpha;8 helix. GH8a contains cellulases, xylanases and other enzymes.
 In GH8b enzymes, the Asp residue is replaced by Asn, and the general base is a Glu residue located in a long loop inserted between &alpha;7 and &alpha;8 helices. GH8b contains chitosanases, licheninases, cellulases and other enzymes.
 The position of the general base in GH8c is unknown.
 == Family Firsts ==

@@ Line 25: / Line 25: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 8 cleave &beta;-1,4 linkages of &beta;-1,4 glucans, xylans (or xylooligosaccharides), chitosans, and lichenans (1,3-1,4-&beta;-D-glucan). All of GH8 members have been found from bacteria, and there are no members from Eukaryotic or Archaeal origin. The majority of the enzymes are [[endo]]-acting enzymes, but one member has an [[exo]]-activity that releases &beta;-D-xylose residues from the reducing end of xylooligosaccharides. The substrate specificities found in GH8 are: chitosanase (EC [{{EClink}}3.2.1.132 3.2.1.132]), cellulase (EC [{{EClink}}3.2.1.4 3.2.1.4]), licheninase (EC [{{EClink}}3.2.1.73 3.2.1.73]), endo-1,4-&beta;-xylanase (EC [{{EClink}}3.2.1.8 3.2.1.8]) and reducing-end-xylose releasing exo-oligoxylanase (EC [{{EClink}}3.2.1.156 3.2.1.156]).
+[[Glycoside hydrolases]] of family 8 cleave &beta;-1,4 linkages of &beta;-1,4 glucans, xylans (or xylooligosaccharides), chitosans, and lichenans (1,3-1,4-&beta;-D-glucan). All of GH8 members have been found from bacteria, and there are no members from Eukaryotic or Archaeal origin. The majority of the enzymes are [[endo]]-acting enzymes, but one member has an [[exo]]-activity that releases &beta;-D-xylose residues from the reducing end of xylooligosaccharides. The substrate specificities found in GH8 are: chitosanase (EC [{{EClink}}3.2.1.132 3.2.1.132]), cellulase (EC [{{EClink}}3.2.1.4 3.2.1.4]), licheninase (EC [{{EClink}}3.2.1.73 3.2.1.73]), endo-1,4-&beta;-xylanase (EC [{{EClink}}3.2.1.8 3.2.1.8]) and reducing-end-xylose releasing exo-oligoxylanase (EC [{{EClink}}3.2.1.156 3.2.1.156]).  GH8 was one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, and was previously known as "Cellulase Family D" <cite>Henrissat1989 Gilkes1991</cite>.
 == Kinetics and Mechanism ==
@@ Line 63: / Line 63: @@
 #Fierobe1993 pmid=8223599
 #Beguin1985 pmid=3980433
 #Petersen2009 pmid=19402614
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH008]]

@@ Line 20: / Line 20: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH8.html
+| colspan="2" |{{CAZyDBlink}}GH8.html
 |}
 </div>

@@ Line 28: / Line 28: @@
 == Kinetics and Mechanism ==
-Enzymes of glycoside hydrolase family 8 are [[inverting]] enzymes, as first shown by Fierobe ''et al.'' who monitored the reaction of endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) using proton NMR spectroscopy <CITE>REF5</CITE>. Hydrolysis by CelA is computationally simulated with QM/MM metadynamics <CITE>REF7</CITE>.
+Enzymes of glycoside hydrolase family 8 are [[inverting]] enzymes, as first shown by Fierobe ''et al.'' who monitored the reaction of endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) using proton NMR spectroscopy <CITE>Fierobe1993</CITE>. Hydrolysis by CelA is computationally simulated with QM/MM metadynamics <CITE>Petersen2009</CITE>.
 == Catalytic Residues ==
-The [[general acid]] (proton donor to the leaving group) was first identified in CelA from ''C. thermocellum'' as Glu95 <cite>REF2</cite>.
+The [[general acid]] (proton donor to the leaving group) was first identified in CelA from ''C. thermocellum'' as Glu95 <cite>Alzari1996</cite>.
-The [[general base]] (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from ''C. thermocellum'' as Asp278 <cite>REF2</cite>.
+The [[general base]] (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from ''C. thermocellum'' as Asp278 <cite>Alzari1996</cite>.
-The [[general base]] of GH8b subfamily was first identified in chitosanase from ''Bacillus'' sp. K17 as Glu309 based on its crystal structure and by making E309Q mutant <cite>REF1</cite>.
+The [[general base]] of GH8b subfamily was first identified in chitosanase from ''Bacillus'' sp. K17 as Glu309 based on its crystal structure and by making E309Q mutant <cite>Adachi2004</cite>.
 == Subfamilies ==
-GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base <cite>REF1</cite>.
+GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base <cite>Adachi2004</cite>.
 GH8a has the general base (Asp) at the N-terminal end of &alpha;8 helix. GH8a contains cellulases, xylanases and other enzymes.
 In GH8b enzymes, the Asp residue is replaced by Asn, and the general base is a Glu residue located in a long loop inserted between &alpha;7 and &alpha;8 helices. GH8b contains chitosanases, licheninases, cellulases and other enzymes.
@@ Line 42: / Line 42: @@
 == Three-dimensional structures ==
-Several three-dimensional structures of GH8 members from bacterial origin have been solved. The first solved 3-D structure was endoglucanase CelA from ''Clostridium thermocellum'' (PDB ID [{{PDBlink}}1cem 1cem]) in 1996 <cite>REF2</cite>. As members of Clan GH-M they have a (&alpha;/&alpha;)<sub>6</sub> fold similar to [[Glycoside Hydrolase Family 48]]. The general acid residue is located at the N-terminal end of &alpha;4 helix. Position of the general base differ among [[#Subfamilies]]. Atomic (0.94 &Aring;) resolution structure of CelA in complex with substrate (PDB ID [{{PDBlink}}1kwf 1kwf]) has been determined <cite>REF3</cite>.
+Several three-dimensional structures of GH8 members from bacterial origin have been solved. The first solved 3-D structure was endoglucanase CelA from ''Clostridium thermocellum'' (PDB ID [{{PDBlink}}1cem 1cem]) in 1996 <cite>Alzari1996</cite>. As members of Clan GH-M they have a (&alpha;/&alpha;)<sub>6</sub> fold similar to [[Glycoside Hydrolase Family 48]]. The general acid residue is located at the N-terminal end of &alpha;4 helix. Position of the general base differ among [[#Subfamilies]]. Atomic (0.94 &Aring;) resolution structure of CelA in complex with substrate (PDB ID [{{PDBlink}}1kwf 1kwf]) has been determined <cite>Guerin2002</cite>.
 == Glycosynthase ==
-Reducing-end-xylose releasing exo-oligoxylanase from ''Bacillus halodurans'' C-125 is the first inverting GH that was converted to glycosynthase by mutating the general base residue <cite>REF4</cite>.
+Reducing-end-xylose releasing exo-oligoxylanase from ''Bacillus halodurans'' C-125 is the first inverting GH that was converted to glycosynthase by mutating the general base residue <cite>Honda2006</cite>.
 == Family Firsts ==
-;First sequence identification: Cellulase (''celA'') from ''Clostridium thermocellum'' <cite>REF6</cite>
+;First sequence identification: Cellulase (''celA'') from ''Clostridium thermocellum'' <cite>Beguin1985</cite>
-;First sterochemistry determination: Endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) <cite>REF5</cite>
+;First sterochemistry determination: Endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) <cite>Fierobe1993</cite>
-;First [[general acid]] residue identification: Cellulase (CelA) from ''Clostridium thermocellum'' <cite>REF2</cite>
+;First [[general acid]] residue identification: Cellulase (CelA) from ''Clostridium thermocellum'' <cite>Alzari1996</cite>
-;First [[general base]] residue identification of GH8a:  Cellulase (CelA) from ''Clostridium thermocellum'' <cite>REF2</cite>
+;First [[general base]] residue identification of GH8a:  Cellulase (CelA) from ''Clostridium thermocellum'' <cite>Alzari1996</cite>
-;First [[general base]] residue identification of GH8b: Chitosanase from ''Bacillus'' sp. K17 by crystal structure and a mutant <cite>REF1</cite>.
+;First [[general base]] residue identification of GH8b: Chitosanase from ''Bacillus'' sp. K17 by crystal structure and a mutant <cite>Adachi2004</cite>.
-;First 3-D structure: Endoglucanase CelA from ''Clostridium thermocellum'' by X-ray crystallography  (PDB ID [{{PDBlink}}1cem 1cem]) <cite>REF2</cite>.
+;First 3-D structure: Endoglucanase CelA from ''Clostridium thermocellum'' by X-ray crystallography  (PDB ID [{{PDBlink}}1cem 1cem]) <cite>Alzari1996</cite>.
 == References ==
 <biblio>
-#REF1 pmid=15465062
+#Adachi2004 pmid=15465062
-#REF2 pmid=8805535
+#Alzari1996 pmid=8805535
-#REF3 pmid=11884144
+#Guerin2002 pmid=11884144
-#REF4 pmid=16301312
+#Honda2006 pmid=16301312
-#REF5 pmid=8223599
+#Fierobe1993 pmid=8223599
-#REF6 pmid=3980433
+#Beguin1985 pmid=3980433
-#REF7 pmid=19402614
+#Petersen2009 pmid=19402614
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH008]]