Glycoside Hydrolase Family 44 - Revision history

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

2021-12-18T21:18:57Z

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

Harry Brumer at 22:41, 18 April 2012

2012-04-18T22:41:42Z

Spencer Williams at 03:08, 14 June 2011

2011-06-14T03:08:59Z

Spencer Williams: /* Kinetics and Mechanism */

2011-01-22T03:40:46Z

Kinetics and Mechanism

Spencer Williams at 03:40, 22 January 2011

2011-01-22T03:40:18Z

Harry Brumer: /* Three-dimensional structures */

2011-01-17T11:00:12Z

Three-dimensional structures

Harry Brumer at 08:56, 17 January 2011

2011-01-17T08:56:11Z

Harry Brumer: /* Three-dimensional structures */

2011-01-17T08:55:37Z

Three-dimensional structures

Harry Brumer: /* Catalytic Residues */

2011-01-17T08:26:51Z

Catalytic Residues

Harry Brumer at 08:23, 17 January 2011

2011-01-17T08:23:39Z

@@ 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]]: ^^^Peter Reilly^^^
+* [[Author]]: [[User:Peter Reilly|Peter Reilly]]
-* [[Responsible Curator]]:  ^^^Peter Reilly^^^
+* [[Responsible Curator]]:  [[User:Peter Reilly|Peter Reilly]]
 ----

@@ Line 58: / Line 58: @@
 #Najmudin2006 pmid=16314409
 #Warner2010 pmid=19915043
-#Warner2011 Warner CD,  Go RM, García-Salinas C, Ford C, and Reilly PJ. ''Kinetic characterization of a glycoside hydrolase family 44 xyloglucanase/endoglucanase from Ruminococcus flavefaciens FD-1''.  Enzyme Microb Technol 2011 Jan 5; 48 (1) 27-32. doi:10.1016/j.enzmictec.2010.08.009 pmid:    .
+#Warner2011 pmid=22112767
 #Henrissat1993 pmid=8352747
 </biblio>

@@ Line 42: / Line 42: @@
 == Three-dimensional structures ==
-The first three-dimensional structure was by Kitago et al., who found a TIM-like barrel domain and a beta-sandwich domain in ''C. thermocellum'' endoglucanase <cite>Kitago2007</cite>. Similar structures were found by Nam et al. <cite>Nam2009</cite> in a protein from a metagenomic library and by Warner et al. <cite>Warner2010</cite> in ''C. acetobutylicum'' endoglucanase. Ca<sup>++</sup> and Zn<sup>++</sup> ions are found as ligands <cite>Kitago2007</cite>.
+The first three-dimensional structure was by Kitago et al., who found a TIM-like barrel domain and a &beta;-sandwich domain in ''C. thermocellum'' endoglucanase <cite>Kitago2007</cite>. Similar structures were found by Nam et al. <cite>Nam2009</cite> in a protein from a metagenomic library and by Warner et al. <cite>Warner2010</cite> in ''C. acetobutylicum'' endoglucanase. Ca<sup>++</sup> and Zn<sup>++</sup> ions are found as ligands <cite>Kitago2007</cite>.
 GH44 was previously known as ''cellulase family J''; see <cite>Henrissat1993</cite> or the [http://expasy.org/cgi-bin/lists?glycosid.txt ExPASy page on GH families].
 == Family Firsts ==
-;First stereochemistry determination: Kitago et al. <cite>Kitago2007</cite> found that ''C. thermocellum'' endoglucanase acts by a [[retaining]] mechanism. They observed that a beta-anomer was preferentially formed during cyclohexaitol hydrolysis.
+;First stereochemistry determination: Kitago et al. <cite>Kitago2007</cite> found that ''C. thermocellum'' endoglucanase acts by a [[retaining]] mechanism. They observed that a &beta;-anomer was preferentially formed during cyclohexaitol hydrolysis.
 ;First [[catalytic nucleophile]] identification: Kitago et al. <cite>Kitago2007</cite>, by testing activity of the ''C. thermocellum'' endoglucanase E359Q mutant.
 ;First [[general acid/base]] residue identification: Kitago et al. <cite>Kitago2007</cite>, by testing activity of the ''C. thermocellum'' endoglucanase E186Q mutant.

@@ Line 33: / Line 33: @@
 == Kinetics and Mechanism ==
-The most complete analyses of GH44 kinetics on various substrates are by Najmudin et al. <cite>Najmudin2006</cite> and by Warner et al. <cite>Warner2010 Warner2011</cite>. GH44 endoglucanases are also xyloglucanases. They hydrolyze longer cellooligosaccharides faster than shorter cellooligosaccharides <cite>Warner2010 Warner2011</cite>. They act asymmetrically on cellooligosaccharides, for instance producing more cellobiose and cellotetraose than cellotriose from cellohexaose <cite>Warner2010 Warner2011</cite>, with substrates bound with more of their residues in negatively-numbered than in positively-numbered subsites. Furthermore, disproportionation occurs, with more cellotetraose than cellobiose formed from cellohexaose, evidently caused by formation of larger unobserved products that are then rapidly hydrolyzed <cite>Warner2010 Warner2011</cite>. GH44 enzymes act with [[retention|retaining]] of anomeric stereochemistry <cite>Kitago2007</cite>, through a [[classical Koshland double-displacement mechanism]] with a covalent bond being formed between the catalytic nucleophile and the anomeric carbon of the substrate, leading to liberation of the leaving group; subsequently, the glycosyl-enzyme is cleaved by water. A [[general acid/base]] residue acts as a general acid in the first step to assist departure of the aglycon; in the second step this residue acts as a general base to assist in deprotonating a nucleophilic water residue.
+The most complete analyses of GH44 kinetics on various substrates are by Najmudin et al. <cite>Najmudin2006</cite> and by Warner et al. <cite>Warner2010 Warner2011</cite>. GH44 endoglucanases are also xyloglucanases. They hydrolyze longer cellooligosaccharides faster than shorter cellooligosaccharides <cite>Warner2010 Warner2011</cite>. They act asymmetrically on cellooligosaccharides, for instance producing more cellobiose and cellotetraose than cellotriose from cellohexaose <cite>Warner2010 Warner2011</cite>, with substrates bound with more of their residues in negatively-numbered than in positively-numbered subsites. Furthermore, disproportionation occurs, with more cellotetraose than cellobiose formed from cellohexaose, evidently caused by formation of larger unobserved products that are then rapidly hydrolyzed <cite>Warner2010 Warner2011</cite>. GH44 enzymes act with [[retaining|retention]] of anomeric stereochemistry <cite>Kitago2007</cite>, through a [[classical Koshland double-displacement mechanism]] with a covalent bond being formed between the catalytic nucleophile and the anomeric carbon of the substrate, leading to liberation of the leaving group; subsequently, the glycosyl-enzyme is cleaved by water. A [[general acid/base]] residue acts as a general acid in the first step to assist departure of the aglycon; in the second step this residue acts as a general base to assist in deprotonating a nucleophilic water residue.
 == Catalytic Residues ==

@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-Active on many substances, including cellooligosaccharides of DP4 and longer, carboxymethylcellulose, xylan, lichenan, Avicel (slightly), and xyloglucan, which appears to be a prime substrate <cite>Najmudin2006 Warner2011</cite>.
+GH44 [[glycoside hydrolases]] are active on many substances, including tetrasaccharide cellooligosaccharides and longer oligomers, carboxymethylcellulose, xylan, lichenan, Avicel (slightly), and xyloglucan, the last of which appears to be a prime substrate <cite>Najmudin2006 Warner2011</cite>.
 == Kinetics and Mechanism ==
-The most complete analyses of kinetics on various substrates are by Najmudin et al. <cite>Najmudin2006</cite> and by Warner et al. <cite>Warner2010 Warner2011</cite>. GH44 endoglucanases are also xyloglucanases. They hydrolyze longer cellooligosaccharides faster than shorter cellooligosaccharides <cite>Warner2010 Warner2011</cite>. They act asymmetrically on cellooligosaccharides, for instance producing more cellobiose and cellotetraose than cellotriose from cellohexaose <cite>Warner2010 Warner2011</cite>, with substrates bound with more of their residues in negatively-numbered than in positively-numbered subsites. Furthermore, disproportionation occurs, with more cellotetraose than cellobiose formed from cellohexaose, evidently caused by formation of larger unobserved products that are then rapidly hydrolyzed <cite>Warner2010 Warner2011</cite>. The mechanism is retaining <cite>Kitago2007</cite>, with a covalent bond being formed between the catalytic nucleophile and the C1' atom, leading to liberation of the leaving group; subsequently, the glycosyl-enzyme is cleaved by water.
+The most complete analyses of GH44 kinetics on various substrates are by Najmudin et al. <cite>Najmudin2006</cite> and by Warner et al. <cite>Warner2010 Warner2011</cite>. GH44 endoglucanases are also xyloglucanases. They hydrolyze longer cellooligosaccharides faster than shorter cellooligosaccharides <cite>Warner2010 Warner2011</cite>. They act asymmetrically on cellooligosaccharides, for instance producing more cellobiose and cellotetraose than cellotriose from cellohexaose <cite>Warner2010 Warner2011</cite>, with substrates bound with more of their residues in negatively-numbered than in positively-numbered subsites. Furthermore, disproportionation occurs, with more cellotetraose than cellobiose formed from cellohexaose, evidently caused by formation of larger unobserved products that are then rapidly hydrolyzed <cite>Warner2010 Warner2011</cite>. GH44 enzymes act with [[retention|retaining]] of anomeric stereochemistry <cite>Kitago2007</cite>, through a [[classical Koshland double-displacement mechanism]] with a covalent bond being formed between the catalytic nucleophile and the anomeric carbon of the substrate, leading to liberation of the leaving group; subsequently, the glycosyl-enzyme is cleaved by water. A [[general acid/base]] residue acts as a general acid in the first step to assist departure of the aglycon; in the second step this residue acts as a general base to assist in deprotonating a nucleophilic water residue.
 == Catalytic Residues ==
 The catalytic residues in this family have been suggested by several experiments with diverse enzymes.  These include:
-* ''' ''Clostridium thermocellum'' endoglucanase:''' Catalytic proton donor/acceptor, Glu186; catalytic nucleophile, Glu359; by soaking the wild-type crystals with cellopentaose or cellohexaose and noting the positions of the residues relative to the reducing end of the cellotetraose product <cite>Kitago2007</cite>, and also by finding no activity with E186Q and E359Q mutants.
+* ''' ''Clostridium thermocellum'' endoglucanase:''' [[General acid/base]], Glu186; [[catalytic nucleophile]], Glu359; by soaking the wild-type crystals with cellopentaose or cellohexaose and noting the positions of the residues relative to the reducing end of the cellotetraose product <cite>Kitago2007</cite>, and also by finding no activity with E186Q and E359Q mutants.
-* '''Protein from metagenomic library:''' Catalytic proton donor/acceptor, Glu221; catalytic nucleophile, Glu393 by location in the active site of the wild-type crystal structure <cite>Nam2009</cite>.
+* '''Protein from metagenomic library:''' [[General acid/base]], Glu221; [[catalytic nucleophile]], Glu393 by location in the active site of the wild-type crystal structure <cite>Nam2009</cite>.
-* ''' ''Clostridium acetobutylicum'' xyloglucanase/endoglucanase:''' Catalytic proton donor/acceptor, Glu180; catalytic nucleophile, Glu352 also by location in the crystal structure of the wild-type enzyme, and by comparison with the ''C. thermocellum'' structure <cite>Warner2010</cite>.
+* ''' ''Clostridium acetobutylicum'' xyloglucanase/endoglucanase:'''  [[General acid/base]], Glu180; [[catalytic nucleophile]], Glu352 also by location in the crystal structure of the wild-type enzyme, and by comparison with the ''C. thermocellum'' structure <cite>Warner2010</cite>.
 == Three-dimensional structures ==
@@ Line 47: / Line 47: @@
 == Family Firsts ==
-;First stereochemistry determination: Kitago et al. <cite>Kitago2007</cite> found that ''C. thermocellum'' endoglucanase acts by a retaining mechanism. They observed that a beta-anomer was preferentially formed during cyclohexaitol hydrolysis.
+;First stereochemistry determination: Kitago et al. <cite>Kitago2007</cite> found that ''C. thermocellum'' endoglucanase acts by a [[retaining]] mechanism. They observed that a beta-anomer was preferentially formed during cyclohexaitol hydrolysis.
-;First catalytic nucleophile identification: Kitago et al. <cite>Kitago2007</cite>, by testing activity of the ''C. thermocellum'' endoglucanase E359Q mutant.
+;First [[catalytic nucleophile]] identification: Kitago et al. <cite>Kitago2007</cite>, by testing activity of the ''C. thermocellum'' endoglucanase E359Q mutant.
-;First general acid/base residue identification: Kitago et al. <cite>Kitago2007</cite>, by testing activity of the ''C. thermocellum'' endoglucanase E186Q mutant.
+;First [[general acid/base]] residue identification: Kitago et al. <cite>Kitago2007</cite>, by testing activity of the ''C. thermocellum'' endoglucanase E186Q mutant.
 ;First 3-D structure: Kitago et al. <cite>Kitago2007</cite> of ''C. thermocellum'' endoglucanase. It had a resolution of 0.96 Å and allowed the identification of the catalytic residues and the mechanism.