Glycoside Hydrolase Family 189 - Revision history

Harry Brumer: added PDB link

2024-02-25T01:29:35Z

added PDB link

Harry Brumer: /* Kinetics and Mechanism */

2024-02-25T01:27:09Z

Kinetics and Mechanism

Harry Brumer: /* Kinetics and Mechanism */

2024-02-25T01:26:08Z

Kinetics and Mechanism

Masahiro Nakajima at 04:02, 24 February 2024

2024-02-24T04:02:05Z

Nobukiyo Tanaka at 03:30, 5 February 2024

2024-02-05T03:30:46Z

Masahiro Nakajima at 00:48, 4 February 2024

2024-02-04T00:48:49Z

Nobukiyo Tanaka at 08:14, 2 February 2024

2024-02-02T08:14:10Z

Nobukiyo Tanaka at 08:06, 2 February 2024

2024-02-02T08:06:48Z

Nobukiyo Tanaka at 07:54, 2 February 2024

2024-02-02T07:54:45Z

Nobukiyo Tanaka at 07:51, 2 February 2024

2024-02-02T07:51:42Z

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 == Three-dimensional structure ==
-The apo-structure of the recombinant TiCGS<sub>Cy</sub> was determined at 3.8 Å by X-ray crystal structure analysis (PDB: 8WY1) <cite>Tanaka2024</cite>. The overall structure comprises a single (α/α)<sub>6</sub>-barrel domain with several inserted α-helices and TiCGS<sub>Cy</sub> has a large active-site pocket (Fig.3) <cite>Tanaka2024</cite>.[[Image:Fig3.png|thumb|widthpx|'''Fig.3 The overall structure of TiCGS<sub>Cy</sub>.'''  ]] Interestingly, although [[GH189]] (= TiCGS<sub>Cy</sub>), [[GH144]] and [[GH162]] enzymes are quite different in their amino acid sequences, their overall structures and the positions of the substrate in their catalytic pockets are similar <cite>Tanaka2024</cite>.
+The apo-structure of the recombinant TiCGS<sub>Cy</sub> was determined at 3.8 Å by X-ray crystal structure analysis (PDB: [{{PDBlink}}8WY1 8WY1]) <cite>Tanaka2024</cite>. The overall structure comprises a single (α/α)<sub>6</sub>-barrel domain with several inserted α-helices and TiCGS<sub>Cy</sub> has a large active-site pocket (Fig.3) <cite>Tanaka2024</cite>.[[Image:Fig3.png|thumb|widthpx|'''Fig.3 The overall structure of TiCGS<sub>Cy</sub>.'''  ]] Interestingly, although [[GH189]] (= TiCGS<sub>Cy</sub>), [[GH144]] and [[GH162]] enzymes are quite different in their amino acid sequences, their overall structures and the positions of the substrate in their catalytic pockets are similar <cite>Tanaka2024</cite>.
 [[GH144]] and [[GH162]] were officially classified as part of clan GH-S in this paper <cite>Tanaka2024</cite>. Although [[GH189]] enzymes share a similar (α/α)<sub>6</sub> fold structure with [[GH144]] and [[GH162]] enzymes, [[GH189]] enzymes have a retaining mechanism unlike [[GH144]] and [[GH162]] enzymes with an inverting mechanism. Due to the fundamental difference in reaction mechanisms, [[GH189]] is not included in clan GH-S; instead, [[GH189]] could be regarded as a member of a potential new GH clan <cite>Tanaka2024</cite>.

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 The reaction products of TiCGS<sub>Cy</sub> were obtained using LβG as the substrate. The β-glucosidase-resistant compounds in the products were purified by size-exclusion chromatography. <sup>1</sup>H-NMR analysis of these purified polysaccharides suggested that they are CβGs. In the chemical shift of <sup>1</sup>H-NMR, no chemical shift derived from an anomeric proton in an α-anomer moiety was detected. This observation clearly demonstrates that TiCGS<sub>Cy</sub> has a retaining mechanism <cite>Tanaka2024</cite>.
-Structural analysis (see [[#Three-Dimensional Structure]] below) and mutational analysis suggest that E1442 of TiCGS<sub>Cy</sub> acts on an anomeric carbon of a glucose moiety at subsite −1 as a nucleophile and E1356 of TiCGS<sub>Cy</sub> acts on a scissile bond of a substrate via 3-hydroxy group of a glucose moiety at subsite +2 as an acid/base <cite>Tanaka2024</cite>. The reaction mechanism of TiCGS<sub>Cy</sub> is noncanonical in that a substrate hydroxy group participates in the catalytic process (Fig.1)<cite>Tanaka2024</cite>.[[Image:Fig1.png.png|thumb|widthpx|'''Fig.1''' '''Catalytic mechanism of TiCGS<sub>Cy</sub>.''' ]]
+Structural analysis (see [[#Three-dimensional Structure]] below) and mutational analysis suggest that E1442 of TiCGS<sub>Cy</sub> acts on an anomeric carbon of a glucose moiety at subsite −1 as a nucleophile and E1356 of TiCGS<sub>Cy</sub> acts on a scissile bond of a substrate via 3-hydroxy group of a glucose moiety at subsite +2 as an acid/base <cite>Tanaka2024</cite>. The reaction mechanism of TiCGS<sub>Cy</sub> is noncanonical in that a substrate hydroxy group participates in the catalytic process (Fig.1)<cite>Tanaka2024</cite>.[[Image:Fig1.png.png|thumb|widthpx|'''Fig.1''' '''Catalytic mechanism of TiCGS<sub>Cy</sub>.''' ]]
 == Catalytic Residues ==

@@ Line 33: / Line 33: @@
 The reaction products of TiCGS<sub>Cy</sub> were obtained using LβG as the substrate. The β-glucosidase-resistant compounds in the products were purified by size-exclusion chromatography. <sup>1</sup>H-NMR analysis of these purified polysaccharides suggested that they are CβGs. In the chemical shift of <sup>1</sup>H-NMR, no chemical shift derived from an anomeric proton in an α-anomer moiety was detected. This observation clearly demonstrates that TiCGS<sub>Cy</sub> has a retaining mechanism <cite>Tanaka2024</cite>.
-Structural analysis (see “Three-dimensional structures” below) and mutational analysis suggest that E1442 of TiCGS<sub>Cy</sub> acts on an anomeric carbon of a glucose moiety at subsite −1 as a nucleophile and E1356 of TiCGS<sub>Cy</sub> acts on a scissile bond of a substrate via 3-hydroxy group of a glucose moiety at subsite +2 as an acid/base <cite>Tanaka2024</cite>. The reaction mechanism of TiCGS<sub>Cy</sub> is noncanonical in that a substrate hydroxy group participates in the catalytic process (Fig.1)<cite>Tanaka2024</cite>.[[Image:Fig1.png.png|thumb|widthpx|'''Fig.1''' '''Catalytic mechanism of TiCGS<sub>Cy</sub>.''' ]]
+Structural analysis (see [[#Three-Dimensional Structure]] below) and mutational analysis suggest that E1442 of TiCGS<sub>Cy</sub> acts on an anomeric carbon of a glucose moiety at subsite −1 as a nucleophile and E1356 of TiCGS<sub>Cy</sub> acts on a scissile bond of a substrate via 3-hydroxy group of a glucose moiety at subsite +2 as an acid/base <cite>Tanaka2024</cite>. The reaction mechanism of TiCGS<sub>Cy</sub> is noncanonical in that a substrate hydroxy group participates in the catalytic process (Fig.1)<cite>Tanaka2024</cite>.[[Image:Fig1.png.png|thumb|widthpx|'''Fig.1''' '''Catalytic mechanism of TiCGS<sub>Cy</sub>.''' ]]
 == Catalytic Residues ==

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 == Kinetics and Mechanism ==
-The reaction products of TiCGS<sub>Cy</sub> were obtained using LβG as the substrate. The β-glucosidase-resistant compounds in the products were purified by size-exclusion chromatography. <sup>1</sup>H-NMR analysis of these purified polysaccharides suggested that they are CβGs. These results clearly demonstrate that TiCGS<sub>Cy</sub> has a retaining mechanism <cite>Tanaka2024</cite>.
+The reaction products of TiCGS<sub>Cy</sub> were obtained using LβG as the substrate. The β-glucosidase-resistant compounds in the products were purified by size-exclusion chromatography. <sup>1</sup>H-NMR analysis of these purified polysaccharides suggested that they are CβGs. In the chemical shift of <sup>1</sup>H-NMR, no chemical shift derived from an anomeric proton in an α-anomer moiety was detected. This observation clearly demonstrates that TiCGS<sub>Cy</sub> has a retaining mechanism <cite>Tanaka2024</cite>.
 Structural analysis (see “Three-dimensional structures” below) and mutational analysis suggest that E1442 of TiCGS<sub>Cy</sub> acts on an anomeric carbon of a glucose moiety at subsite −1 as a nucleophile and E1356 of TiCGS<sub>Cy</sub> acts on a scissile bond of a substrate via 3-hydroxy group of a glucose moiety at subsite +2 as an acid/base <cite>Tanaka2024</cite>. The reaction mechanism of TiCGS<sub>Cy</sub> is noncanonical in that a substrate hydroxy group participates in the catalytic process (Fig.1)<cite>Tanaka2024</cite>.[[Image:Fig1.png.png|thumb|widthpx|'''Fig.1''' '''Catalytic mechanism of TiCGS<sub>Cy</sub>.''' ]]

@@ Line 33: / Line 33: @@
 The reaction products of TiCGS<sub>Cy</sub> were obtained using LβG as the substrate. The β-glucosidase-resistant compounds in the products were purified by size-exclusion chromatography. <sup>1</sup>H-NMR analysis of these purified polysaccharides suggested that they are CβGs. These results clearly demonstrate that TiCGS<sub>Cy</sub> has a retaining mechanism <cite>Tanaka2024</cite>.
-Structural analysis (see “Three-dimensional structures” below) and mutational analysis suggest that E1442 of TiCGS<sub>Cy</sub> acts on an anomeric carbon of a glucose moiety at subsite −1 as a nucleophile and E1356 of TiCGS<sub>Cy</sub> acts on a scissile bond of a substrate via 3-hydroxy group of a glucose moiety at subsite +2 as an acid/base <cite>Tanaka2024</cite>. The reaction mechanism of TiCGS<sub>Cy</sub> is noncanonical in that a substrate hydroxy group participates in the catalytic process (Fig.1)<cite>Tanaka2024</cite>.[[Image:Fig1.png|thumb|widthpx|'''Fig.1''' '''Catalytic mechanism of TiCGS<sub>Cy</sub>.''' ]]
+Structural analysis (see “Three-dimensional structures” below) and mutational analysis suggest that E1442 of TiCGS<sub>Cy</sub> acts on an anomeric carbon of a glucose moiety at subsite −1 as a nucleophile and E1356 of TiCGS<sub>Cy</sub> acts on a scissile bond of a substrate via 3-hydroxy group of a glucose moiety at subsite +2 as an acid/base <cite>Tanaka2024</cite>. The reaction mechanism of TiCGS<sub>Cy</sub> is noncanonical in that a substrate hydroxy group participates in the catalytic process (Fig.1)<cite>Tanaka2024</cite>.[[Image:Fig1.png.png|thumb|widthpx|'''Fig.1''' '''Catalytic mechanism of TiCGS<sub>Cy</sub>.''' ]]
 == Catalytic Residues ==

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]s: [[User:Tomoko Masaike|Tomoko Masaike]], [[User:Masahiro Nakajima|Masahiro Nakajima]], and [[User:Nobukiyo Tanaka|Nobukiyo Tanaka]]
 * [[Responsible Curator]]:  [[User:Masahiro Nakajima|Masahiro Nakajima]]

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 |-
 |'''Mechanism'''
-|retaining
+|Retaining
 |-
 |'''Active site residues'''
-|known
+|Known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''

@@ Line 10: / Line 10: @@
 |-
 |{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH189'''
-[[User:Nobukiyo Tanaka|Nobukiyo Tanaka]] ([[User talk:Nobukiyo Tanaka|talk]]) 23:43, 1 February 2024 (PST)
+|-
 |'''Clan'''
 |GH-x