Carbohydrate Esterase Family 3 - Revision history

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

2021-12-18T21:16:30Z

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

Harry Brumer: Changed "Clan" to "fold" in table header

2021-04-06T15:39:37Z

Changed "Clan" to "fold" in table header

Joel Weadge: /* Three-dimensional structures */

2020-12-02T19:40:22Z

Three-dimensional structures

Joel Weadge: /* Three-dimensional structures */

2020-12-02T19:39:48Z

Three-dimensional structures

Joel Weadge: /* Kinetics and Mechanism */

2020-12-02T19:39:04Z

Kinetics and Mechanism

Stefen Stangherlin: /* Kinetics and Mechanism */

2020-06-16T22:50:30Z

Kinetics and Mechanism

Stefen Stangherlin at 18:53, 16 June 2020

2020-06-16T18:53:10Z

Joel Weadge at 17:07, 10 June 2020

2020-06-10T17:07:38Z

Joel Weadge at 17:05, 10 June 2020

2020-06-10T17:05:26Z

Joel Weadge at 17:02, 10 June 2020

2020-06-10T17:02:41Z

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Stefen Stangherlin^^^
+* [[Author]]: [[User:Stefen Stangherlin|Stefen Stangherlin]]
-* [[Responsible Curator]]s:  ^^^Michael Suits^^^ and ^^^Joel Weadge^^^
+* [[Responsible Curator]]s:  [[User:Michael Suits|Michael Suits]] and [[User:Joel Weadge|Joel Weadge]]
 ----

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 |{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family CE3'''
 |-
-|'''Clan'''
+|'''Fold'''
 |(α/β/α)-Sandwich
 |-

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 == Three-dimensional structures ==
-The CE3 family has a number of enzymes that have been structurally resolved; ''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]) (see Fig. 1) and ''Ct''Ces3-1 from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum'') ([{{PDBlink}}2VPT PDB ID 2VPT]). Both structures adopt an (α/β/α)-sandwich fold typical of the SGNH hydrolase family. The (α/β/α)-sandwich contains five central parallel β-strands forming a curved β-sheet, which is flanked by 5-6 α-helices <cite>Correia2008 Uechi2016</cite>. Additionally, both structures contain a calcium binding loop motif (DXVGX<sub>7</sub>DX<sub>n</sub>(D/N)) located above the N-terminal end of the central β-strand (β2) <cite>Watanabe2015</cite>. This binding motif is conserved across all currently characterized CE3s. A coordinated zinc ion was also observed next to a calcium ion in a ''Tc''AE206_S10A variant ([{{PDBlink}}5B5L PDB ID 5B5L]), however this was attributed to the use of ZnSO<sub>4</sub> in the crystallization conditions <cite>Uechi2016</cite>. Unique to ''Tc''AE206 is a disulfide bond formed near the N-terminus (see Fig. 1) that is thought to position the catalytic Ser by stabilizing neighbouring areas, including a β-turn (β1) that involves the catalytic Ser <cite>Uechi2016 Watanabe2015</cite>.
+The CE3 family has a number of enzymes that have been structurally resolved. Examples include ''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]) (see Fig. 1) and ''Ct''Ces3-1 from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum'') ([{{PDBlink}}2VPT PDB ID 2VPT]). Both structures adopt an (α/β/α)-sandwich fold typical of the SGNH hydrolase family. The (α/β/α)-sandwich contains five central parallel β-strands forming a curved β-sheet, which is flanked by 5-6 α-helices <cite>Correia2008 Uechi2016</cite>. Additionally, both structures contain a calcium binding loop motif (DXVGX<sub>7</sub>DX<sub>n</sub>(D/N)) located above the N-terminal end of the central β-strand (β2) <cite>Watanabe2015</cite>. This binding motif is conserved across all currently characterized CE3s. A coordinated zinc ion was also observed next to a calcium ion in a ''Tc''AE206_S10A variant ([{{PDBlink}}5B5L PDB ID 5B5L]), however this was attributed to the use of ZnSO<sub>4</sub> in the crystallization conditions <cite>Uechi2016</cite>. Unique to ''Tc''AE206 is a disulfide bond formed near the N-terminus (see Fig. 1) that is thought to position the catalytic Ser by stabilizing neighbouring areas, including a β-turn (β1) that involves the catalytic Ser <cite>Uechi2016 Watanabe2015</cite>.
 == Family Firsts ==

@@ Line 40: / Line 40: @@
 == Three-dimensional structures ==
-Two members of the CE3 family have been structurally resolved, ''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]) (see Fig. 1) and ''Ct''Ces3-1 from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum'') ([{{PDBlink}}2VPT PDB ID 2VPT]). Both structures adopt an (α/β/α)-sandwich fold typical of the SGNH hydrolase family. The (α/β/α)-sandwich contains five central parallel β-strands forming a curved β-sheet, which is flanked by 5-6 α-helices <cite>Correia2008 Uechi2016</cite>. Additionally, both structures contain a calcium binding loop motif (DXVGX<sub>7</sub>DX<sub>n</sub>(D/N)) located above the N-terminal end of the central β-strand (β2) <cite>Watanabe2015</cite>. This binding motif is conserved across all currently characterized CE3s. A coordinated zinc ion was also observed next to a calcium ion in a ''Tc''AE206_S10A variant ([{{PDBlink}}5B5L PDB ID 5B5L]), however this was attributed to the use of ZnSO<sub>4</sub> in the crystallization conditions <cite>Uechi2016</cite>. Unique to ''Tc''AE206 is a disulfide bond formed near the N-terminus (see Fig. 1) that is thought to position the catalytic Ser by stabilizing neighbouring areas, including a β-turn (β1) that involves the catalytic Ser <cite>Uechi2016 Watanabe2015</cite>.
+The CE3 family has a number of enzymes that have been structurally resolved; ''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]) (see Fig. 1) and ''Ct''Ces3-1 from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum'') ([{{PDBlink}}2VPT PDB ID 2VPT]). Both structures adopt an (α/β/α)-sandwich fold typical of the SGNH hydrolase family. The (α/β/α)-sandwich contains five central parallel β-strands forming a curved β-sheet, which is flanked by 5-6 α-helices <cite>Correia2008 Uechi2016</cite>. Additionally, both structures contain a calcium binding loop motif (DXVGX<sub>7</sub>DX<sub>n</sub>(D/N)) located above the N-terminal end of the central β-strand (β2) <cite>Watanabe2015</cite>. This binding motif is conserved across all currently characterized CE3s. A coordinated zinc ion was also observed next to a calcium ion in a ''Tc''AE206_S10A variant ([{{PDBlink}}5B5L PDB ID 5B5L]), however this was attributed to the use of ZnSO<sub>4</sub> in the crystallization conditions <cite>Uechi2016</cite>. Unique to ''Tc''AE206 is a disulfide bond formed near the N-terminus (see Fig. 1) that is thought to position the catalytic Ser by stabilizing neighbouring areas, including a β-turn (β1) that involves the catalytic Ser <cite>Uechi2016 Watanabe2015</cite>.
 == Family Firsts ==

@@ Line 37: / Line 37: @@
 CE3 esterases catalyze the hydrolysis of O-linked acetyl groups from xylan oligo- and poly-saccharides. The Block V His residue abstracts a proton from the Block I Ser, rendering it nucleophilic, which attacks the electrophilic carbonyl carbon of the acetyl group of the xylan substrate; generating a tetrahedral oxyanion intermediate that is stabilized by the backbone amides of the Block I Ser and Block II Gly, as well as the sidechain amide of the Block III Asn, together forming the oxyanion hole in the active site <cite>Uechi2016</cite>. Collapse of the oxyanion intermediate results in the formation of a transient acyl-enzyme intermediate and alcohol by-product <cite>Uechi2016</cite>. A hydrolytic water molecule is then deprotonated by the Block V His residue, and attacks the acyl-enzyme intermediate; hydrolyzing the bond and releasing acetate and the free enzyme <cite>Uechi2016</cite>. In the process, the Ser (Block I) is re-protonated and ready for another catalytic cycle.
-The kinetics for two enzymes from the CE3 family have been studied. ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) was found to have a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 2.5 and 1.2 mM<sup>-1</sup>s<sup>-1</sup> for ''p''-nitrophenyl acetate (''p''NP-Ac) and acetylated xylan, respectively <cite>Correia2008</cite>. In other studies, ''Tc''AE206 ([{{PDBlink}}5B5S PDB ID 5B5S]) was not assayed against acetylated xylan, but the ''k''<sub>cat</sub>/''K''<sub>M</sub> with ''p''NP-Ac and ''p''-nitrophenyl butyrate (''p''NP-B) were reported as 44.7 and 4.1 mM<sup>-1</sup>s<sup>-1</sup>, respectively, while no activity was detected with ''p''‐nitrophenyl octanoate (''p''NP-O) as the substrate <cite>Watanabe2015</cite>.
+The kinetics for enzymes from the CE3 family have been examined. For example, ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) was found to have a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 2.5 and 1.2 mM<sup>-1</sup>s<sup>-1</sup> for ''p''-nitrophenyl acetate (''p''NP-Ac) and acetylated xylan, respectively <cite>Correia2008</cite>. In other studies, ''Tc''AE206 ([{{PDBlink}}5B5S PDB ID 5B5S]) was not assayed against acetylated xylan, but the ''k''<sub>cat</sub>/''K''<sub>M</sub> with ''p''NP-Ac and ''p''-nitrophenyl butyrate (''p''NP-B) were reported as 44.7 and 4.1 mM<sup>-1</sup>s<sup>-1</sup>, respectively, while no activity was detected with ''p''‐nitrophenyl octanoate (''p''NP-O) as the substrate <cite>Watanabe2015</cite>.
 == Three-dimensional structures ==

@@ Line 35: / Line 35: @@
 == Kinetics and Mechanism ==
-CE3 esterases catalyze the hydrolysis of O-linked acetyl groups from xylan oligo- and poly-saccharides. The Block V His residue abstracts a proton from the Block I Ser, rendering it nucleophilic, which attacks the electrophilic carbonyl carbon of the acetyl group of the xylan substrate; generating a tetrahedral oxyanion transition state that is stabilized by the backbone amides of the Block I Ser and Block II Gly, as well as the sidechain amide of the Block III Asn, together forming the oxyanion hole in the active site <cite>Uechi2016</cite>. Collapse of the oxyanion intermediate results in the formation of a transient acyl-enzyme intermediate and alcohol by-product <cite>Uechi2016</cite>. A hydrolytic water molecule is then deprotonated by the Block V His residue, and attacks the acyl-enzyme intermediate; hydrolyzing the bond and releasing acetate and the free enzyme <cite>Uechi2016</cite>. In the process, the Ser (Block I) is re-protonated and ready for another catalytic cycle.
+CE3 esterases catalyze the hydrolysis of O-linked acetyl groups from xylan oligo- and poly-saccharides. The Block V His residue abstracts a proton from the Block I Ser, rendering it nucleophilic, which attacks the electrophilic carbonyl carbon of the acetyl group of the xylan substrate; generating a tetrahedral oxyanion intermediate that is stabilized by the backbone amides of the Block I Ser and Block II Gly, as well as the sidechain amide of the Block III Asn, together forming the oxyanion hole in the active site <cite>Uechi2016</cite>. Collapse of the oxyanion intermediate results in the formation of a transient acyl-enzyme intermediate and alcohol by-product <cite>Uechi2016</cite>. A hydrolytic water molecule is then deprotonated by the Block V His residue, and attacks the acyl-enzyme intermediate; hydrolyzing the bond and releasing acetate and the free enzyme <cite>Uechi2016</cite>. In the process, the Ser (Block I) is re-protonated and ready for another catalytic cycle.
 The kinetics for two enzymes from the CE3 family have been studied. ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) was found to have a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 2.5 and 1.2 mM<sup>-1</sup>s<sup>-1</sup> for ''p''-nitrophenyl acetate (''p''NP-Ac) and acetylated xylan, respectively <cite>Correia2008</cite>. In other studies, ''Tc''AE206 ([{{PDBlink}}5B5S PDB ID 5B5S]) was not assayed against acetylated xylan, but the ''k''<sub>cat</sub>/''K''<sub>M</sub> with ''p''NP-Ac and ''p''-nitropheyl butyrate (''p''NP-B) were reported as 44.7 and 4.1 mM<sup>-1</sup>s<sup>-1</sup>, respectively, while no activity was detected with ''p''‐nitrophenyl octanoate (''p''NP-O) as the substrate <cite>Watanabe2015</cite>.