Glycoside Hydrolase Family 19 - Revision history

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

2021-12-18T21:19:09Z

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

Harry Brumer: updated CAZyDBlink

2012-09-10T16:33:25Z

updated CAZyDBlink

Spencer Williams at 10:14, 11 June 2011

2011-06-11T10:14:53Z

Spencer Williams at 11:56, 14 June 2010

2010-06-14T11:56:25Z

Spencer Williams at 11:57, 20 April 2010

2010-04-20T11:57:08Z

Harry Brumer: Undo revision 4449 by Harry Brumer (Talk)

2010-04-16T13:20:52Z

Undo revision 4449 by Harry Brumer (Talk)

Harry Brumer at 13:19, 16 April 2010

2010-04-16T13:19:56Z

Harry Brumer at 12:42, 16 April 2010

2010-04-16T12:42:52Z

Harry Brumer at 12:41, 16 April 2010

2010-04-16T12:41:58Z

Harry Brumer at 12:38, 16 April 2010

2010-04-16T12:38:35Z

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 {{CuratorApproved}}
-* [[Author]]: ^^^Vincent Eijsink^^^
+* [[Author]]: [[User:Vincent Eijsink|Vincent Eijsink]]
-* [[Responsible Curator]]:  ^^^Vincent Eijsink^^^
+* [[Responsible Curator]]:  [[User:Vincent Eijsink|Vincent Eijsink]]
 ----

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 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH19.html
+| colspan="2" |{{CAZyDBlink}}GH19.html
 |}
 </div>

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 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 19 are [[endo]]-acting enzymes that hydrolyze glycosidic bonds within chitin, an insoluble polymer of beta-1,4-linked ''N''-acetyl-D-glucosamine (GlcNAc) and are thus referred to as chitinases (EC [{{EClink}}3.2.1.14 3.2.1.14]). These enzymes were originally identified in plants. In an older classification system for plant chitinases, comprising both [[GH18]] and GH19 chitinases, family 19 enzymes comprise classes I, II and IV. In 1996, the first bacterial family 19 chitinase was described <cite>Ohno1996</cite>. In addition to cleaving chitin, GH19 chitinases cleave soluble oligomers of beta-1,4-linked ''N''-acetyl-D-glucosamine. For some plant enzymes lysozyme activity has been demonstrated. Currently available data suggest that GH19 enzymes are not particularly effective in degrading crystalline chitin (compared to certain members of the GH18 chitinase family), especially enzymes that lack CBMs. On the other hand GH19 enzymes are highly active on chitosans (= partially deacetylated chitin) with high degrees of acetylation, even if they lack a CBM <cite>Kawase2006 Heggset2009</cite>. Detailed studies on GH19 chitinases from ''Streptomyces'' (class IV; <cite>Heggset2009</cite>) and rice (''Oryza sativa''; Class I; <cite>Sasaki2006</cite>) have revealed that productive binding requires a GlcNAc to be bound in subsites -2 and +1, whereas deacetylated GlcNAc (GlcN) is tolerated in subsites -1 and +2.
+[[Glycoside hydrolases]] of family 19 are [[endo]]-acting enzymes that hydrolyze glycosidic bonds within chitin, an insoluble polymer of &beta;-1,4-linked ''N''-acetyl-D-glucosamine (GlcNAc) and are thus referred to as chitinases (EC [{{EClink}}3.2.1.14 3.2.1.14]). These enzymes were originally identified in plants. In an older classification system for plant chitinases, comprising both [[GH18]] and GH19 chitinases, family 19 enzymes comprise classes I, II and IV. In 1996, the first bacterial family 19 chitinase was described <cite>Ohno1996</cite>. In addition to cleaving chitin, GH19 chitinases cleave soluble oligomers of &beta;-1,4-linked ''N''-acetyl-D-glucosamine. For some plant enzymes lysozyme activity has been demonstrated. Currently available data suggest that GH19 enzymes are not particularly effective in degrading crystalline chitin (compared to certain members of the GH18 chitinase family), especially enzymes that lack CBMs. On the other hand GH19 enzymes are highly active on chitosans (= partially deacetylated chitin) with high degrees of acetylation, even if they lack a CBM <cite>Kawase2006 Heggset2009</cite>. Detailed studies on GH19 chitinases from ''Streptomyces'' (class IV; <cite>Heggset2009</cite>) and rice (''Oryza sativa''; Class I; <cite>Sasaki2006</cite>) have revealed that productive binding requires a GlcNAc to be bound in subsites -2 and +1, whereas deacetylated GlcNAc (GlcN) is tolerated in subsites -1 and +2.
 == Kinetics and Mechanism ==

@@ Line 27: / Line 27: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 19 hydrolyze glycosidic bonds in chitin, an insoluble polymer of beta-1,4-linked ''N''-acetyl-D-glucosamine (GlcNAc) and are thus referred to as chitinases (EC [{{EClink}}3.2.1.14 3.2.1.14]). These enzymes were originally identified in plants. In an older classification system for plant chitinases, comprising both [[GH18]] and GH19 chitinases, family 19 enzymes comprise classes I, II and IV. In 1996, the first bacterial family 19 chitinase was described <cite>Ohno1996</cite>. In addition to cleaving chitin, GH19 chitinases cleave soluble oligomers of beta-1,4-linked ''N''-acetyl-D-glucosamine. For some plant enzymes lysozyme activity has been demonstrated. Currently available data suggest that GH19 enzymes are not particularly effective in degrading crystalline chitin (compared to certain members of the GH18 chitinase family), especially enzymes that lack CBMs. On the other hand GH19 enzymes are highly active on chitosans (= partially deacetylated chitin) with high degrees of acetylation, even if they lack a CBM <cite>Kawase2006 Heggset2009</cite>. Detailed studies on GH19 chitinases from ''Streptomyces'' (class IV; <cite>Heggset2009</cite>) and rice (''Oryza sativa''; Class I; <cite>Sasaki2006</cite>) have revealed that productive binding requires a GlcNAc to be bound in subsites -2 and +1, whereas deacetylated GlcNAc (GlcN) is tolerated in subsites -1 and +2.
+[[Glycoside hydrolases]] of family 19 are [[endo]]-acting enzymes that hydrolyze glycosidic bonds within chitin, an insoluble polymer of beta-1,4-linked ''N''-acetyl-D-glucosamine (GlcNAc) and are thus referred to as chitinases (EC [{{EClink}}3.2.1.14 3.2.1.14]). These enzymes were originally identified in plants. In an older classification system for plant chitinases, comprising both [[GH18]] and GH19 chitinases, family 19 enzymes comprise classes I, II and IV. In 1996, the first bacterial family 19 chitinase was described <cite>Ohno1996</cite>. In addition to cleaving chitin, GH19 chitinases cleave soluble oligomers of beta-1,4-linked ''N''-acetyl-D-glucosamine. For some plant enzymes lysozyme activity has been demonstrated. Currently available data suggest that GH19 enzymes are not particularly effective in degrading crystalline chitin (compared to certain members of the GH18 chitinase family), especially enzymes that lack CBMs. On the other hand GH19 enzymes are highly active on chitosans (= partially deacetylated chitin) with high degrees of acetylation, even if they lack a CBM <cite>Kawase2006 Heggset2009</cite>. Detailed studies on GH19 chitinases from ''Streptomyces'' (class IV; <cite>Heggset2009</cite>) and rice (''Oryza sativa''; Class I; <cite>Sasaki2006</cite>) have revealed that productive binding requires a GlcNAc to be bound in subsites -2 and +1, whereas deacetylated GlcNAc (GlcN) is tolerated in subsites -1 and +2.
 == Kinetics and Mechanism ==
@@ Line 34: / Line 34: @@
 == Catalytic Residues ==
 [[Image:GH19_detail.PNG|thumb|right|300px|'''Conserved residues surrounding the catalytic acid, Glu67, in the family 19 papaya chitinase (PDB ID [{{PDBlink}}3cql 3cql]).''' Amino acid side chains are shown in stick representation. Hydrogen bonds are shown as dashed lines with distances indicated in Å. A GlcNAc<sub>2</sub> unit binding in the -1 and +1 subsites is shown in narrow stick representation and an arrow indicates the position of the glycosidic oxygen. The sugar ring substituents are not shown in order to make the figure clearer. The structure of this complex comes from a model described in reference <cite>Huet2008</cite>. The picture is taken from reference <cite>Hoell2010</cite>.]]
-The catalytic residues are two glutamates. Although there still is limited structural information underpinning details of the inverting catalytic mechanism, there is considerable support for the notion that a glutamate located at the end of the third alpha helix (Glu 67 in the barley enzyme) acts as the catalytic [[general acid]], whereas another glutamate located in a more variable loop-like structure (Glu89 in the barley enzyme) acts as the catalytic [[general base]]<cite>Hart1993 Andersen1997 Hoell2006 Huet2008</cite>.
+The catalytic residues are two glutamates. Although there still is limited structural information underpinning details of the [[inverting]] catalytic mechanism, there is considerable support for the notion that a glutamate located at the end of the third alpha helix (Glu 67 in the barley enzyme) acts as the catalytic [[general acid]], whereas another glutamate located in a more variable loop-like structure (Glu89 in the barley enzyme) acts as the catalytic [[general base]]<cite>Hart1993 Andersen1997 Hoell2006 Huet2008</cite>.
 It has been shown that at least two more conserved charged residues are crucial for catalysis. These residues, Glu203 and Arg215 in barley chitinase, form a triad together with the catalytic acid Glu67 <cite>Ohnishi2005</cite> (see Figure). Interestingly, a similarly complex electrostatic interaction network is present in family [[GH46]] chitosanases <cite>Fukamizo2000 Lacombe2009</cite> with whom the family 19 enzymes share some overall structural similarity (see below).

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 == Substrate specificities ==
-Glycoside hydrolases of family 19 hydrolyze glycoside bonds in chitin, an insoluble polymer of beta-1,4-linked ''N''-acetyl-D-glucosamine (GlcNAc) and are thus referred to as chitinases (EC [{{EClink}}3.2.1.14 3.2.1.14]). These enzymes were originally identified in plants. In an older classification system for plant chitinases, comprising both [[GH18]] and GH19 chitinases, family 19 enzymes comprise classes I, II and IV. In 1996, the first bacterial family 19 chitinase was described <cite>Ohno1996</cite>. In addition to cleaving chitin, GH19 chitinases cleave soluble oligomers of beta-1,4-linked ''N''-acetyl-D-glucosamine. For some plant enzymes lysozyme activity has been demonstrated. Currently available data suggest that GH19 enzymes are not particularly effective in degrading crystalline chitin (compared to certain members of the GH18 chitinase family), especially enzymes that lack CBMs. On the other hand GH19 enzymes are highly active on chitosans (= partially deacetylated chitin) with high degrees of acetylation, even if they lack a CBM <cite>Kawase2006 Heggset2009</cite>. Detailed studies on GH19 chitinases from ''Streptomyces'' (class IV; <cite>Heggset2009</cite>) and rice (''Oryza sativa''; Class I; <cite>Sasaki2006</cite>) have revealed that productive binding requires a GlcNAc to be bound in subsites -2 and +1, whereas deacetylated GlcNAc (GlcN) is tolerated in subsites -1 and +2.
+[[Glycoside hydrolases]] of family 19 hydrolyze glycosidic bonds in chitin, an insoluble polymer of beta-1,4-linked ''N''-acetyl-D-glucosamine (GlcNAc) and are thus referred to as chitinases (EC [{{EClink}}3.2.1.14 3.2.1.14]). These enzymes were originally identified in plants. In an older classification system for plant chitinases, comprising both [[GH18]] and GH19 chitinases, family 19 enzymes comprise classes I, II and IV. In 1996, the first bacterial family 19 chitinase was described <cite>Ohno1996</cite>. In addition to cleaving chitin, GH19 chitinases cleave soluble oligomers of beta-1,4-linked ''N''-acetyl-D-glucosamine. For some plant enzymes lysozyme activity has been demonstrated. Currently available data suggest that GH19 enzymes are not particularly effective in degrading crystalline chitin (compared to certain members of the GH18 chitinase family), especially enzymes that lack CBMs. On the other hand GH19 enzymes are highly active on chitosans (= partially deacetylated chitin) with high degrees of acetylation, even if they lack a CBM <cite>Kawase2006 Heggset2009</cite>. Detailed studies on GH19 chitinases from ''Streptomyces'' (class IV; <cite>Heggset2009</cite>) and rice (''Oryza sativa''; Class I; <cite>Sasaki2006</cite>) have revealed that productive binding requires a GlcNAc to be bound in subsites -2 and +1, whereas deacetylated GlcNAc (GlcN) is tolerated in subsites -1 and +2.
 == Kinetics and Mechanism ==
-Family 19 enzymes employ an inverting mechanism, as determined by NMR <cite>Fukamizo1995</cite> and HPLC <cite>Iseli1996</cite>. Both structural characteristics (see below) and available biochemical data <cite>Sasaki2006 Heggset2009</cite> suggest that GH19 chitinases are non-processive endo-acting enzymes. Kinetic data for the conversion of polymeric and oligomeric substrates have been described in several studies. In some studies, kinetic data have been used to derive subsite binding affinties (e.g. <cite>Honda1998 Sasaki2003</cite>).
+Family 19 enzymes employ an [[inverting]] mechanism, as determined by NMR <cite>Fukamizo1995</cite> and HPLC analysis<cite>Iseli1996</cite>. Both structural characteristics (see below) and available biochemical data <cite>Sasaki2006 Heggset2009</cite> suggest that GH19 chitinases are non-processive [[endo]]-acting enzymes. Kinetic data for the conversion of polymeric and oligomeric substrates have been described in several studies. In some studies, kinetic data have been used to derive subsite binding affinties (e.g. <cite>Honda1998 Sasaki2003</cite>).
 == Catalytic Residues ==
 [[Image:GH19_detail.PNG|thumb|right|300px|'''Conserved residues surrounding the catalytic acid, Glu67, in the family 19 papaya chitinase (PDB ID [{{PDBlink}}3cql 3cql]).''' Amino acid side chains are shown in stick representation. Hydrogen bonds are shown as dashed lines with distances indicated in Å. A GlcNAc<sub>2</sub> unit binding in the -1 and +1 subsites is shown in narrow stick representation and an arrow indicates the position of the glycosidic oxygen. The sugar ring substituents are not shown in order to make the figure clearer. The structure of this complex comes from a model described in reference <cite>Huet2008</cite>. The picture is taken from reference <cite>Hoell2010</cite>.]]
-The catalytic residues are two glutamates. Although there still is limited structural information underpinning details of the inverting catalytic mechanism, there is considerable support for the notion that a glutamate located at the end of the third alpha helix (Glu 67 in the barley enzyme) acts as the catalytic acid, whereas another glutamate located in a more variable loop-like structure (Glu89 in the barley enzyme) acts as the catalytic base <cite>Hart1993 Andersen1997 Hoell2006 Huet2008</cite>.
+The catalytic residues are two glutamates. Although there still is limited structural information underpinning details of the inverting catalytic mechanism, there is considerable support for the notion that a glutamate located at the end of the third alpha helix (Glu 67 in the barley enzyme) acts as the catalytic [[general acid]], whereas another glutamate located in a more variable loop-like structure (Glu89 in the barley enzyme) acts as the catalytic [[general base]]<cite>Hart1993 Andersen1997 Hoell2006 Huet2008</cite>.
 It has been shown that at least two more conserved charged residues are crucial for catalysis. These residues, Glu203 and Arg215 in barley chitinase, form a triad together with the catalytic acid Glu67 <cite>Ohnishi2005</cite> (see Figure). Interestingly, a similarly complex electrostatic interaction network is present in family [[GH46]] chitosanases <cite>Fukamizo2000 Lacombe2009</cite> with whom the family 19 enzymes share some overall structural similarity (see below).
@@ Line 57: / Line 57: @@
 ;First stereochemistry determination: Yam chitinase, by NMR <cite>Fukamizo1995</cite> and Bean chitinase, by HPLC <cite>Iseli1996</cite>.
-;First general base residue identification: Chitinase from barley; determination by site-directed mutagenesis <cite>Andersen1997</cite>, structural analysis <cite>Hart1993</cite> and modelling <cite>Brameld1998</cite>. Additional support from structure determination and modelling of a papaya chitinase <cite>Huet2008</cite>.
+;First [[general base]] residue identification: Chitinase from barley; determination by site-directed mutagenesis <cite>Andersen1997</cite>, structural analysis <cite>Hart1993</cite> and modelling <cite>Brameld1998</cite>. Additional support from structure determination and modelling of a papaya chitinase <cite>Huet2008</cite>.
-;First general acid residue identification: Chitinase from barley; determination by site-directed mutagenesis <cite>Andersen1997</cite>, structural analysis <cite>Hart1993</cite> and modelling <cite>Brameld1998</cite>. Additional support from structure determination and modelling of a papaya chitinase <cite>Huet2008</cite>.
+;First [[general acid]] residue identification: Chitinase from barley; determination by site-directed mutagenesis <cite>Andersen1997</cite>, structural analysis <cite>Hart1993</cite> and modelling <cite>Brameld1998</cite>. Additional support from structure determination and modelling of a papaya chitinase <cite>Huet2008</cite>.
 ;First 3-D structure: Barley chitinase <cite>Hart1993</cite>.

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 There is no structural information for GH19 enzymes in complex with their substrate. In 2008, Huet et al published <cite>Huet2008</cite> the structure of a complex of papaya family 19 chitinase with GlcNAc units bound in the -2 and +1 subsites. This structure has been used to build a plausible model of a complex with (GlcNAc)<sub>4</sub>. This is the first structure (half experimental, half modeled) of an enzyme-substrate complex.
 === Structure images ===
 [[Image:GH19both.PNG|thumb|left|560px|'''Structures of the barley GH19 chitinase (left; PDB ID [{{PDBlink}}1cns 1cns])and ChiG from ''S. coelicolor'' (right; PDB ID [{{PDBlink}}2cjl 2cjl]).''' The side chains of the catalytic acids are shown in green. Additionally, the side chains of several residues that are (putatively) involved in substrate binding and catalysis are shown in red and purple. The picture is taken from reference <cite>Hoell2006</cite>.]]

← Older revision		Revision as of 12:42, 16 April 2010
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	There is no structural information for GH19 enzymes in complex with their substrate. In 2008, Huet et al published <cite>Huet2008</cite> the structure of a complex of papaya family 19 chitinase with GlcNAc units bound in the -2 and +1 subsites. This structure has been used to build a plausible model of a complex with (GlcNAc)<sub>4</sub>. This is the first structure (half experimental, half modeled) of an enzyme-substrate complex.		There is no structural information for GH19 enzymes in complex with their substrate. In 2008, Huet et al published <cite>Huet2008</cite> the structure of a complex of papaya family 19 chitinase with GlcNAc units bound in the -2 and +1 subsites. This structure has been used to build a plausible model of a complex with (GlcNAc)<sub>4</sub>. This is the first structure (half experimental, half modeled) of an enzyme-substrate complex.

		+	=== Structure images ===
	[[Image:GH19both.PNG\|thumb\|left\|560px\|'''Structures of the barley GH19 chitinase (left; PDB ID [{{PDBlink}}1cns 1cns])and ChiG from ''S. coelicolor'' (right; PDB ID [{{PDBlink}}2cjl 2cjl]).''' The side chains of the catalytic acids are shown in green. Additionally, the side chains of several residues that are (putatively) involved in substrate binding and catalysis are shown in red and purple. The picture is taken from reference <cite>Hoell2006</cite>.]]		[[Image:GH19both.PNG\|thumb\|left\|560px\|'''Structures of the barley GH19 chitinase (left; PDB ID [{{PDBlink}}1cns 1cns])and ChiG from ''S. coelicolor'' (right; PDB ID [{{PDBlink}}2cjl 2cjl]).''' The side chains of the catalytic acids are shown in green. Additionally, the side chains of several residues that are (putatively) involved in substrate binding and catalysis are shown in red and purple. The picture is taken from reference <cite>Hoell2006</cite>.]]

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 </div>
 <!-- This is the end of the table -->
 == Substrate specificities ==