Talk:Glycoside Hydrolase Family 3 - Revision history

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

2021-12-18T21:10:37Z

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

Brian Mark at 01:37, 11 April 2013

2013-04-11T01:37:50Z

Harry Brumer: /* Comment from ^^^Shinya Fushinobu^^^, Sept. 2011 = */

2012-12-15T02:17:14Z

Comment from ^^^Shinya Fushinobu^^^, Sept. 2011 =

Harry Brumer at 02:17, 15 December 2012

2012-12-15T02:17:03Z

Harry Brumer: /* References */

2012-12-15T02:15:04Z

References

Harry Brumer: /* Update to Catalytic Residues section needed? */

2012-12-15T01:58:30Z

Update to Catalytic Residues section needed?

Harry Brumer: /* Update to Catalytic Residues section needed? */ new section

2012-12-15T01:55:46Z

Update to Catalytic Residues section needed?: new section

Shinya Fushinobu: Created page with "Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)₈ domain. pmid: 208..."

2011-09-02T11:28:49Z

Created page with "Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 208..."

New page

Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 20826810.

@@ Line 1: / Line 1: @@
-== Comment from ^^^Brian Mark^^^, April 2013 ==
+== Comment from [[User:Brian Mark|Brian Mark]], April 2013 ==
 The GH3 page has received a comprehensive update.  The following comments have been addressed.  Thank-you for the input!
-== Comment from ^^^Shinya Fushinobu^^^, Sept. 2011 ==
+== Comment from [[User:Shinya Fushinobu|Shinya Fushinobu]], Sept. 2011 ==
 Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (&beta;/&alpha;)<sub>8</sub> domain. pmid: 20826810.

← Older revision		Revision as of 01:37, 11 April 2013
Line 1:		Line 1:
		+
		+	== Comment from ^^^Brian Mark^^^, April 2013 ==
		+	The GH3 page has received a comprehensive update. The following comments have been addressed. Thank-you for the input!
		+
	== Comment from ^^^Shinya Fushinobu^^^, Sept. 2011 ==		== Comment from ^^^Shinya Fushinobu^^^, Sept. 2011 ==
	Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 20826810.		Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 20826810.

← Older revision		Revision as of 02:17, 15 December 2012
Line 1:		Line 1:
−	== Comment from ^^^Shinya Fushinobu^^^, Sept. 2011 ===	+	== Comment from ^^^Shinya Fushinobu^^^, Sept. 2011 ==
	Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 20826810.		Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 20826810.

@@ Line 1: / Line 1: @@
 Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (&beta;/&alpha;)<sub>8</sub> domain. pmid: 20826810.
 == Update to Catalytic Residues section needed? ==
 Given the growing amount of information about the identity of the GH3 catalytic residues - and in particular the acid/base - in different enzymes/subfamilies, I wonder if a update of this section isn't needed?
@@ Line 8: / Line 8: @@
 === References ===
 <biblio>
 #Thongpoo2012 pmid=23201198 // Subfamily 4, 3-D homology model, mutagenesis, kinetic analysis, pH profile, azide rescue

@@ Line 10: / Line 10: @@
 <biblio>
-#Thongpoo2012 pmid=23201198 // Subfamily 4, via kinetic analysis & azide rescue
+#Thongpoo2012 pmid=23201198 // Subfamily 4, 3-D homology model, mutagenesis, kinetic analysis, pH profile, azide rescue
-#Bacik2012 pmid=23177201 // NagZ subfamily, ligand complex
+#Bacik2012 pmid=23177201 // 1-domain Nag, experimental structure, ligand complex, mobile loop bearing acid/base
-#Litzinger2010 pmid=20826810 // NagZ sunfamily, kinetic analysis
+#Litzinger2010 pmid=20826810 // 2-domain Nag, strucuture, mutagenesis, kinetic analysis, pH profile, azide rescue unsuccessful
-#Pozzo2010 pmid=20138890 // Subfamily 5
+#Pozzo2010 pmid=20138890 // Subfamily 5, experimental structure, complexes, reduced Km for mutant with PNP-Glc
-#Yoshida2010 pmid=20662765 // Subfamily 5
+#Yoshida2010 pmid=20662765 // Subfamily 5, experimental structure, product complex
-#Li2006 pmid=16717412 //double-check
+#Li2006 pmid=16717412 //Nag - relevant? Appears to be mis-identification.
-#Paal2004 pmid=14561218 //Subfamily 5
+#Paal2004 pmid=14561218 //Subfamily 5, kinetic analysis, pH profile, azide rescue
-#Chir2002 pmid=11978178 // Subfamily 5
+#Chir2002 pmid=11978178 // Subfamily 5, Glu-473 labelled by N-bromoacetyl-beta-d-glucosylamine
-#Li2002 pmid=11851422 // Nag - relevant? Mis-identification.
+#Li2002 pmid=11851422 //Subfamily 5, kinetic analysis, pH profile, azide rescue
 #Vocadlo2000 pmid=10625486
 #Dan2000 pmid=10671536

@@ Line 3: / Line 3: @@
 == Update to Catalytic Residues section needed? ==
-Given the growing amount of information about the identity of the GH3 catalytic residues, and in particular the acid/base, in different enzymes/subfamilies, I wonder if a update of this section isn't needed?
+Given the growing amount of information about the identity of the GH3 catalytic residues - and in particular the acid/base - in different enzymes/subfamilies, I wonder if a update of this section isn't needed?
 Here are some key acid/base ID references <cite>Thongpoo2012 Bacik2012 Litzinger2010 Pozzo2010 Yoshida2010 Li2006 Paal2004 Chir2002 Li2002</cite>, one of which also confirms the catalytic nucleophile <cite>Paal2004</cite>.  These references are nucleophile-specific studies <cite>Vocadlo2000 Dan2000</cite>:

← Older revision		Revision as of 01:55, 15 December 2012
Line 1:		Line 1:
	Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 20826810.		Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)<sub>8</sub> domain. pmid: 20826810.
		+
		+	== Update to Catalytic Residues section needed? ==
		+
		+	Given the growing amount of information about the identity of the GH3 catalytic residues, and in particular the acid/base, in different enzymes/subfamilies, I wonder if a update of this section isn't needed?
		+
		+	Here are some key acid/base ID references <cite>Thongpoo2012 Bacik2012 Litzinger2010 Pozzo2010 Yoshida2010 Li2006 Paal2004 Chir2002 Li2002</cite>, one of which also confirms the catalytic nucleophile <cite>Paal2004</cite>. These references are nucleophile-specific studies <cite>Vocadlo2000 Dan2000</cite>:
		+
		+	=== References ===
		+
		+	<biblio>
		+	#Thongpoo2012 pmid=23201198 // Subfamily 4, via kinetic analysis & azide rescue
		+	#Bacik2012 pmid=23177201 // NagZ subfamily, ligand complex
		+	#Litzinger2010 pmid=20826810 // NagZ sunfamily, kinetic analysis
		+	#Pozzo2010 pmid=20138890 // Subfamily 5
		+	#Yoshida2010 pmid=20662765 // Subfamily 5
		+	#Li2006 pmid=16717412 //double-check
		+	#Paal2004 pmid=14561218 //Subfamily 5
		+	#Chir2002 pmid=11978178 // Subfamily 5
		+	#Li2002 pmid=11851422 // Nag - relevant? Mis-identification.
		+	#Vocadlo2000 pmid=10625486
		+	#Dan2000 pmid=10671536
		+	</biblio>
		+
		+
		+	[[User:Harry Brumer\|Harry Brumer]] ([[User talk:Harry Brumer\|talk]]) 17:55, 14 December 2012 (PST)