Glycoside Hydrolase Family 46 - Revision history

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

2021-12-18T21:20:39Z

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

Harry Brumer: updated CAZyDBlink

2012-09-10T16:37:59Z

updated CAZyDBlink

Spencer Williams at 03:09, 14 June 2011

2011-06-14T03:09:34Z

Harry Brumer at 07:49, 24 February 2010

2010-02-24T07:49:20Z

Ryszard Brzezinski at 21:57, 23 February 2010

2010-02-23T21:57:31Z

Marie-Eve Lacombe-Harvey at 17:22, 16 February 2010

2010-02-16T17:22:37Z

Marie-Eve Lacombe-Harvey at 16:52, 16 February 2010

2010-02-16T16:52:33Z

Marie-Eve Lacombe-Harvey at 16:51, 16 February 2010

2010-02-16T16:51:48Z

Marie-Eve Lacombe-Harvey at 16:50, 16 February 2010

2010-02-16T16:50:08Z

Spencer Williams at 10:54, 12 February 2010

2010-02-12T10:54:03Z

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 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]s: ^^^Ryszard Brzezinski^^^ and ^^^Marie-Ève Lacombe-Harvey^^^
+* [[Author]]s: [[User:Ryszard Brzezinski|Ryszard Brzezinski]] and [[User:Marie-Ève Lacombe-Harvey|Marie-Ève Lacombe-Harvey]]
-* [[Responsible Curator]]:  ^^^Ryszard Brzezinski^^^
+* [[Responsible Curator]]:  [[User:Ryszard Brzezinski|Ryszard Brzezinski]]
 ----

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 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH46.html
+| colspan="2" |{{CAZyDBlink}}GH46.html
 |}
 </div>

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 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 46 are essentially all ''endo''-beta-1,4-chitosanases (EC [{{EClink}}3.2.1.132 3.2.1.132]) that hydrolyze various links in chitosan, a polymer of beta-1,4-linked D-glucosamine (GlcN) units with a variable content (mostly 0 - 35%) of N-acetyl-D-glucosamine (GlcNAc) <cite>Yabuki1988 Boucher1992</cite>. Among the four types of links occurring between these two kinds of subunits in chitosan, all the enzymes examined for their cleavage specificity acted upon the GlcN-GlcN links. In addition, the chitosanase from ''Bacillus circulans'' MH-K1 recognized also GlcN-GlcNAc links <cite>Mitsutomi1996</cite>, while the chitosanase from ''Streptomyces'' sp. N174 recognized the GlcNAc-GlcN links <cite>Fukamizo1995</cite>.
+[[Glycoside hydrolases]] of family 46 are essentially all ''endo''-&beta;-1,4-chitosanases (EC [{{EClink}}3.2.1.132 3.2.1.132]) that hydrolyze various links in chitosan, a polymer of &beta;-1,4-linked D-glucosamine (GlcN) units with a variable content (mostly 0 - 35%) of N-acetyl-D-glucosamine (GlcNAc) <cite>Yabuki1988 Boucher1992</cite>. Among the four types of links occurring between these two kinds of subunits in chitosan, all the enzymes examined for their cleavage specificity acted upon the GlcN-GlcN links. In addition, the chitosanase from ''Bacillus circulans'' MH-K1 recognized also GlcN-GlcNAc links <cite>Mitsutomi1996</cite>, while the chitosanase from ''Streptomyces'' sp. N174 recognized the GlcNAc-GlcN links <cite>Fukamizo1995</cite>.
 == Kinetics and Mechanism ==
@@ Line 39: / Line 39: @@
 == Three-dimensional structures ==
 [[File:csn_entire_5a.png|200px|thumb|right|3D structure of the chitosanase from ''Streptomyces'' sp. N174]]
-Two structures have been solved using X-ray crystallography, for the chitosanases from Streptomyces sp. N174 <cite>Marcotte1996</cite> and from Bacillus circulans MH-K1 (wild-type enzyme <cite>Saito1999</cite> and mutant K218P <cite>Fukamizo2005</cite>. These enzymes have essentially an alpha-helical fold, with two globular domains separated by the active site cleft for substrate binding. The cleft is bordered on the upper face by a three-stranded beta-sheet. The structure of GH46 enzymes is similar to the 3D fold of the well studied lysozyme of bacteriophage T4 of ''Escherichia coli'' belonging to family GH24 <cite>Marcotte1996</cite> and, to some extent, to the structures of lysozymes from families GH22, GH23 as well the chitinases from family GH19 <cite>Monzingo1996</cite>. These five families are sometimes grouped in the "lysozyme superfamily" <cite>Holm1994 Lacombe-Harvey2009</cite>.
+Two structures have been solved using X-ray crystallography, for the chitosanases from Streptomyces sp. N174 <cite>Marcotte1996</cite> and from Bacillus circulans MH-K1 (wild-type enzyme <cite>Saito1999</cite> and mutant K218P <cite>Fukamizo2005</cite>. These enzymes have essentially an &alpha;-helical fold, with two globular domains separated by the active site cleft for substrate binding. The cleft is bordered on the upper face by a three-stranded &beta;-sheet. The structure of GH46 enzymes is similar to the 3D fold of the well studied lysozyme of bacteriophage T4 of ''Escherichia coli'' belonging to family GH24 <cite>Marcotte1996</cite> and, to some extent, to the structures of lysozymes from families GH22, GH23 as well the chitinases from family GH19 <cite>Monzingo1996</cite>. These five families are sometimes grouped in the "lysozyme superfamily" <cite>Holm1994 Lacombe-Harvey2009</cite>.
 The crystal structures, completed by site-directed mutagenesis have also revealed several residues involved in substrate binding <cite>Marcotte1996 Fukamizo2005 Tremblay2001 Katsumi2005</cite>. For the chitosanase from ''Streptomyces'' sp N174, the mode of binding of a GlcN hexasaccharide was established as being in conformity with a symmetrical 3+3 model, based on the analysis of products of hydrolysis  <cite>Tremblay2001</cite>.

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 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Ryszard Brzezinski^^^; ^^^Marie-Ève Lacombe-Harvey^^^
+* [[Author]]s: ^^^Ryszard Brzezinski^^^ and ^^^Marie-Ève Lacombe-Harvey^^^
 * [[Responsible Curator]]:  ^^^Ryszard Brzezinski^^^
 ----

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 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Ryszard Brzezinski^^^
+* [[Author]]: ^^^Ryszard Brzezinski^^^; ^^^Marie-Ève Lacombe-Harvey^^^
 * [[Responsible Curator]]:  ^^^Ryszard Brzezinski^^^
 ----

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 == Three-dimensional structures ==
 Two structures have been solved using X-ray crystallography, for the chitosanases from Streptomyces sp. N174 <cite>Marcotte1996</cite> and from Bacillus circulans MH-K1 (wild-type enzyme <cite>Saito1999</cite> and mutant K218P <cite>Fukamizo2005</cite>. These enzymes have essentially an alpha-helical fold, with two globular domains separated by the active site cleft for substrate binding. The cleft is bordered on the upper face by a three-stranded beta-sheet. The structure of GH46 enzymes is similar to the 3D fold of the well studied lysozyme of bacteriophage T4 of ''Escherichia coli'' belonging to family GH24 <cite>Marcotte1996</cite> and, to some extent, to the structures of lysozymes from families GH22, GH23 as well the chitinases from family GH19 <cite>Monzingo1996</cite>. These five families are sometimes grouped in the "lysozyme superfamily" <cite>Holm1994 Lacombe-Harvey2009</cite>.
 The crystal structures, completed by site-directed mutagenesis have also revealed several residues involved in substrate binding <cite>Marcotte1996 Fukamizo2005 Tremblay2001 Katsumi2005</cite>. For the chitosanase from ''Streptomyces'' sp N174, the mode of binding of a GlcN hexasaccharide was established as being in conformity with a symmetrical 3+3 model, based on the analysis of products of hydrolysis  <cite>Tremblay2001</cite>.
-[[File:csn_entire_5.png|200px|thumb|right|3D structure]]
 == Family Firsts ==
 ;First primary sequence determination: Chitosanase from ''Bacillus circulans'' MH-K1 <cite>Ando1992</cite>.

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 == Substrate specificities ==
-Glycoside hydrolases of family 46 are essentially ''endo''-beta-1,4-chitosanases (EC [{{EClink}}3.2.1.132 3.2.1.132]) that hydrolyze various links in chitosan, a polymer of beta-1,4-linked D-glucosamine (GlcN) units with a variable content (mostly 0 - 35%) of N-acetyl-D-glucosamine (GlcNAc) <cite>Yabuki1988 Boucher1992</cite>. Among the four types of links occurring between these two kinds of subunits in chitosan, all the enzymes examined for their cleavage specificity recognized productively the GlcN-GlcN links. In addition, the chitosanase from ''Bacillus circulans'' MH-K1 recognized also GlcN-GlcNAc links <cite>Mitsutomi1996</cite>, while the chitosanase from ''Streptomyces'' sp. N174 recognized the GlcNAc-GlcN links <cite>Fukamizo1995</cite>.
+[[Glycoside hydrolases]] of family 46 are essentially all ''endo''-beta-1,4-chitosanases (EC [{{EClink}}3.2.1.132 3.2.1.132]) that hydrolyze various links in chitosan, a polymer of beta-1,4-linked D-glucosamine (GlcN) units with a variable content (mostly 0 - 35%) of N-acetyl-D-glucosamine (GlcNAc) <cite>Yabuki1988 Boucher1992</cite>. Among the four types of links occurring between these two kinds of subunits in chitosan, all the enzymes examined for their cleavage specificity acted upon the GlcN-GlcN links. In addition, the chitosanase from ''Bacillus circulans'' MH-K1 recognized also GlcN-GlcNAc links <cite>Mitsutomi1996</cite>, while the chitosanase from ''Streptomyces'' sp. N174 recognized the GlcNAc-GlcN links <cite>Fukamizo1995</cite>.
 == Kinetics and Mechanism ==
-Family GH46 enzymes utilize an inverting mechanism, as shown by NMR <cite>Fukamizo1995</cite>.
+Family GH46 enzymes utilize an [[inverting]] mechanism, as shown by NMR <cite>Fukamizo1995</cite>.
 == Catalytic Residues ==
-The catalytic residues have been identified by site-directed mutagenesis and crystallography in the chitosanase from Streptomyces sp. N174. The general acid residue is Glu22 in the sequence SSA<u>'''E'''</u>NSS, while Asp40 (DIG<u>'''D'''</u>GRG) is the general base residue <cite>Boucher1995 Marcotte1996</cite>. The latter could activate the nucleophilic water molecule with assistance from residue Thr45 (RGY<u>'''T'''</u>GGI) <cite>Lacombe-Harvey2009</cite>. Analysis of sequence alignments as well as crystallographic evidence showed that the same function is played by residues Glu37 (in the sequence NKP'''<u>E</u>'''QDD) , Asp55 (DIE<u>'''D'''</u>ERG) and Thr60 (RGY'''<u>T</u>'''IGL) in the chitosanase from ''Bacillus circulans'' MH-K1 <cite>Saito1999</cite>.
+The catalytic residues have been identified by site-directed mutagenesis and crystallography in the chitosanase from Streptomyces sp. N174. The [[general acid]] residue is Glu22 in the sequence SSA<u>'''E'''</u>NSS, while Asp40 (DIG<u>'''D'''</u>GRG) is the [[general base]] residue <cite>Boucher1995 Marcotte1996</cite>. The latter could activate the nucleophilic water molecule with assistance from residue Thr45 (RGY<u>'''T'''</u>GGI) <cite>Lacombe-Harvey2009</cite>. Analysis of sequence alignments as well as crystallographic evidence showed that the same function is played by residues Glu37 (in the sequence NKP'''<u>E</u>'''QDD) , Asp55 (DIE<u>'''D'''</u>ERG) and Thr60 (RGY'''<u>T</u>'''IGL) in the chitosanase from ''Bacillus circulans'' MH-K1 <cite>Saito1999</cite>.
 == Three-dimensional structures ==
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 ;First primary sequence determination: Chitosanase from ''Bacillus circulans'' MH-K1 <cite>Ando1992</cite>.
 ;First sterochemistry determination: Chitosanase from ''Streptomyces'' sp. N174 by NMR <cite>Fukamizo1995</cite>.
-;First general base residue identification: Chitosanase from ''Streptomyces'' sp. N174 by sequence conservation and mutagenesis <cite>Boucher1995</cite> and by X-ray crystallography <cite>Marcotte1996</cite>.
+;First [[general base]] residue identification: Chitosanase from ''Streptomyces'' sp. N174 by sequence conservation and mutagenesis <cite>Boucher1995</cite> and by X-ray crystallography <cite>Marcotte1996</cite>.
-;First general acid residue identification: Chitosanase from ''Streptomyces'' sp. N174 by sequence conservation and mutagenesis <cite>Boucher1995</cite> and by X-ray crystallography <cite>Marcotte1996</cite>.
+;First [[general acid]] residue identification: Chitosanase from ''Streptomyces'' sp. N174 by sequence conservation and mutagenesis <cite>Boucher1995</cite> and by X-ray crystallography <cite>Marcotte1996</cite>.
 ;First 3-D structure: Chitosanase from ''Streptomyces'' sp. N174 by X-ray crystallography <cite>Marcotte1996</cite>.