Glycoside Hydrolase Family 42 - Revision history

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

2021-12-18T21:16:53Z

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

Harry Brumer: /* Three-dimensional structures */

2020-04-09T00:50:32Z

Three-dimensional structures

Harry Brumer: updated CAZyDBlink

2012-06-25T22:54:27Z

updated CAZyDBlink

Harry Brumer at 14:40, 28 November 2009

2009-11-28T14:40:46Z

Spencer Williams: /* Kinetics and Mechanism */

2009-11-04T11:05:46Z

Kinetics and Mechanism

Spencer Williams at 11:05, 4 November 2009

2009-11-04T11:05:15Z

Marco Moracci at 07:50, 4 November 2009

2009-11-04T07:50:10Z

Harry Brumer: /* Catalytic Residues */

2009-11-03T18:51:14Z

Catalytic Residues

Harry Brumer: /* Kinetics and Mechanism */

2009-11-03T18:49:01Z

Kinetics and Mechanism

Harry Brumer: /* Substrate specificities */

2009-11-03T18:48:13Z

Substrate specificities

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Marco Moracci^^^
+* [[Author]]: [[User:Marco Moracci|Marco Moracci]]
-* [[Responsible Curator]]:  ^^^Marco Moracci^^^
+* [[Responsible Curator]]:  [[User:Marco Moracci|Marco Moracci]]
 ----

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 == Three-dimensional structures ==
-Only one three-dimensional structure is available for enzymes belonging to Family GH42, that of the β-galactosidase from ''T. thermophilus'' A4, which was solved at 1.6 Å and 2.2 Å resolution in the free and galactose-bound enzyme, respectively <cite>10</cite>. As members of Clan GH-A, Family GH42 enzymes show the catalytic dyad at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) within a domain showing a classical (&alpha;/β)<sub>8</sub> TIM barrel (domain A). This catalytic domain contains a metal-binding site with a Zn atom that is not related with the binding of galactose and that thereby seems to have structural features. Domain B, showing a &alpha;/β fold domain, is involved in the native trimer formation while the function of domain C (β fold domain) is unknown.
+The three-dimensional structure of the β-galactosidase from ''T. thermophilus'' A4 was solved at 1.6 Å and 2.2 Å resolution in the free and galactose-bound enzyme, respectively <cite>10</cite>. As members of Clan GH-A, Family GH42 enzymes present the catalytic dyad at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) within a domain showing a classical (&alpha;/β)<sub>8</sub> TIM barrel (domain A). This catalytic domain contains a metal-binding site with a Zn atom that is not related with the binding of galactose and that thereby seems to have structural features. Domain B, showing a &alpha;/β fold domain, is involved in the native trimer formation while the function of domain C (β fold domain) is unknown.
 == Family Firsts ==

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 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH42.html
+| colspan="2" |{{CAZyDBlink}}GH42.html
 |}
 </div>

← Older revision		Revision as of 14:40, 28 November 2009
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		+	{{CuratorApproved}}
	* [[Author]]: ^^^Marco Moracci^^^		* [[Author]]: ^^^Marco Moracci^^^
	* [[Responsible Curator]]: ^^^Marco Moracci^^^		* [[Responsible Curator]]: ^^^Marco Moracci^^^

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 == Kinetics and Mechanism ==
-Family GH42 β-galactosidase are [[retaining]] enzymes, as first shown by NMR <cite>10</cite>, and follow the [[classical Koshland double-displacement]] mechanism.  Enzymes whose reaction mechanism has been well studied include the β-galactosidase from ''Thermus thermophilus'' A4, YesZ from ''Bacillus subtilis'', and the enzyme from ''Alicyclobacillus acidocaldarius''.
+Family GH42 β-galactosidase are [[retaining]] enzymes, as first shown by NMR <cite>10</cite>, and follow the [[classical Koshland double-displacement mechanism]].  Enzymes whose reaction mechanism has been well studied include the β-galactosidase from ''Thermus thermophilus'' A4, YesZ from ''Bacillus subtilis'', and the enzyme from ''Alicyclobacillus acidocaldarius''.
 == Catalytic Residues ==

@@ Line 26: / Line 26: @@
 == Substrate specificities ==
-The best known enzymatic activity for glycoside hydrolases in this family, at the current time, is β-galactosidase (EC 3.2.1.23), however, other commonly found activities are &alpha;-L-arabinosidase (EC 3.2.1.55) and β-D-fucosidase   (EC 3.2.1.38) with both ''K<sub>m</sub>'' and ''k<sub>cat</sub>'' of the same order of magnitude for the different substrates <cite>1, 2</cite>. Apparently, these enzymes show strict specificity for axial C4-OH groups.
+The most common activity for [[glycoside hydrolase]]s of this family are β-galactosidases (EC 3.2.1.23), however, other commonly found activities are &alpha;-L-arabinosidase (EC 3.2.1.55) and β-D-fucosidase   (EC 3.2.1.38) with both ''K''<sub>M</sub> and ''k''<sub>cat</sub> values being of the same order of magnitude for the different substrates <cite>1, 2</cite>. Apparently, these enzymes show strict specificity for axial C4-OH groups.
-Interestingly, Family GH42 enzymes have been identified only in unicellular organisms, mainly from prokaryotes (in majority bacteria), and with few examples from archaea and fungi. GH42 enzymes are active on lactose <cite>2, 3, 4, 5</cite> and transgalactosylation was also observed with production of galactooligosaccharides <cite>6</cite>. However, several GH42 enzymes are extracted from diverse habitats where lactose would not be present and they are very active on galactooligosaccharides and galactans <cite>1, 7, 8, 9</cite>, suggesting that these enzymes would be involved ''in vivo'' in plant cell wall degradation. This function would be performed in cooperation with family [[GH53]] galactanases, often encoded from genes adjacent to GH42 genes <cite>9</cite>, and with cellulosome <cite>1</cite>.<sub></sub>
+Family GH42 enzymes have been identified only in unicellular organisms, mainly from prokaryotes (in majority bacteria), and with a few examples from archaea and fungi. GH42 enzymes are active on lactose <cite>2, 3, 4, 5</cite> and transgalactosylation was observed with production of galactooligosaccharides <cite>6</cite>. However, several GH42 enzymes are extracted from diverse habitats where lactose would not be present and they are very active on galactooligosaccharides and galactans <cite>1, 7, 8, 9</cite>, suggesting that these enzymes would be involved ''in vivo'' in plant cell wall degradation. This function could be performed in cooperation with family [[GH53]] galactanases, often encoded from genes adjacent to GH42 genes <cite>9</cite>, and with cellulosome <cite>1</cite>.<sub></sub>
-However, the activity of GH42 enzymes on lactose and also lactulose <cite>2</cite> has interesting applicative potential for the removal of the former from dairy products and to monitor lactulose concentration during heat treatment leading to UHT milk.
+The activity of GH42 enzymes on lactose and also lactulose <cite>2</cite> has interesting potential for the removal of the former from dairy products and to monitor lactulose concentration during heat treatment leading to UHT milk.
 == Kinetics and Mechanism ==
-Family GH42 β-galactosidase are [[retaining]] enzymes, as first shown by NMR <cite>10</cite>, and follow the classical Koshland double-displacement mechanism.  Enzymes whose reaction mechanism has been well studied include the β-galactosidase from ''Thermus thermophilus'' A4, YesZ from ''Bacillus subtilis'', and the enzyme from ''Alicyclobacillus acidocaldarius''.
+Family GH42 β-galactosidase are [[retaining]] enzymes, as first shown by NMR <cite>10</cite>, and follow the [[classical Koshland double-displacement]] mechanism.  Enzymes whose reaction mechanism has been well studied include the β-galactosidase from ''Thermus thermophilus'' A4, YesZ from ''Bacillus subtilis'', and the enzyme from ''Alicyclobacillus acidocaldarius''.
 == Catalytic Residues ==
-The [[catalytic nucleophile]] was first identified in the ''B. subtilis'' YesZ β-galactosidase as Glu295 through the use of a mechanism-based inhibitor that allowed trapping of the 2-deoxy-2-fluorogalactosyl-enzyme intermediate and subsequent peptide mapping. Interestingly, these experiments were performed on the mutant of the inferred acid/base, which  was more sensitive to the inhibitor <cite>11</cite>. The [[general acid/base]] catalyst was first identified as Glu157 in the β-galactosidase from ''A. acidocaldarius'' through detailed mechanistic analysis and azide rescue experiments of a mutant in that position <cite>2</cite>.
+The [[catalytic nucleophile]] was first identified in the ''B. subtilis'' YesZ β-galactosidase as Glu295 through the use of a mechanism-based inhibitor that allowed trapping of the 2-deoxy-2-fluorogalactosyl-enzyme [[intermediate]] and subsequent peptide mapping. These experiments were performed on the mutant of the inferred acid/base, which was more sensitive to the inhibitor <cite>11</cite>. The [[general acid/base]] catalyst was first identified as Glu157 in the β-galactosidase from ''A. acidocaldarius'' through detailed mechanistic analysis and azide rescue experiments of a mutant in that position <cite>2</cite>.
 == Three-dimensional structures ==
-So far only one three-dimensional structure is available for enzymes belonging to Family GH42, that of the β-galactosidase from ''T. thermophilus'' A4, which was solved at 1.6 Å and 2.2 Å resolution in the free and galactose-bound enzyme, respectively <cite>10</cite>. As members of Clan GH-A, Family GH42 enzymes show the catalytic dyad at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) within a domain showing a classical (&alpha;/β)<sub>8</sub> TIM barrel (domain A). This catalytic domain contains a metal-binding site with a Zn atom that is not related with the binding of galactose and that thereby seems to have structural features. Domain B, showing a &alpha;/β fold domain, is involved in the native trimer formation while the function of domain C (β fold domain) is unknown.
+Only one three-dimensional structure is available for enzymes belonging to Family GH42, that of the β-galactosidase from ''T. thermophilus'' A4, which was solved at 1.6 Å and 2.2 Å resolution in the free and galactose-bound enzyme, respectively <cite>10</cite>. As members of Clan GH-A, Family GH42 enzymes show the catalytic dyad at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) within a domain showing a classical (&alpha;/β)<sub>8</sub> TIM barrel (domain A). This catalytic domain contains a metal-binding site with a Zn atom that is not related with the binding of galactose and that thereby seems to have structural features. Domain B, showing a &alpha;/β fold domain, is involved in the native trimer formation while the function of domain C (β fold domain) is unknown.
 == Family Firsts ==