https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&feed=atom&action=history
Glycoside Hydrolase Family 28 - Revision history
2024-03-29T09:34:38Z
Revision history for this page on the wiki
MediaWiki 1.35.10
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=16633&oldid=prev
Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"
2021-12-18T21:18:46Z
<p>Text replacement - "\^\^\^(.*)\^\^\^" to "<a href="/index.php?title=User:$1&action=edit&redlink=1" class="new" title="User:$1 (page does not exist)">$1</a>"</p>
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Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=14950&oldid=prev
Kazune Tamura at 22:55, 22 May 2020
2020-05-22T22:55:19Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:55, 22 May 2020</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The structure of rhamnogalacturonase (RGase A) from ''Aspergillus aculeatus'' <cite>4</cite> revealed the signature parallel &beta;-helix architecture common to several pectin active enzymes including family 1 pectate lyases ([[PL1]]). The GH28 enzymes are distinguished from the lyases by having four, not three, parallel &beta;-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of &beta;-helix having ten <del class="diffchange diffchange-inline">tuns</del>, not eleven <cite>5</cite>. The structure of exopolygalacturonase from ''Yersinia enterocolitica'' shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The structure of rhamnogalacturonase (RGase A) from ''Aspergillus aculeatus'' <cite>4</cite> revealed the signature parallel &beta;-helix architecture common to several pectin active enzymes including family 1 pectate lyases ([[PL1]]). The GH28 enzymes are distinguished from the lyases by having four, not three, parallel &beta;-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of &beta;-helix having ten <ins class="diffchange diffchange-inline">turns</ins>, not eleven <cite>5</cite>. The structure of exopolygalacturonase from ''Yersinia enterocolitica'' shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
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Kazune Tamura
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=10913&oldid=prev
Harry Brumer: /* Three-dimensional structures */
2015-08-07T00:18:54Z
<p><span dir="auto"><span class="autocomment">Three-dimensional structures</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 00:18, 7 August 2015</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The structure of rhamnogalacturonase (RGase A) from ''Aspergillus aculeatus'' <cite>4</cite> revealed the signature parallel &beta;-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by having four, not three, parallel &beta;-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of &beta;-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from ''Yersinia enterocolitica'' shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The structure of rhamnogalacturonase (RGase A) from ''Aspergillus aculeatus'' <cite>4</cite> revealed the signature parallel &beta;-helix architecture common to several pectin active enzymes including family 1 pectate lyases <ins class="diffchange diffchange-inline">([[PL1]])</ins>. The GH28 enzymes are distinguished from the lyases by having four, not three, parallel &beta;-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of &beta;-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from ''Yersinia enterocolitica'' shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
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Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=9350&oldid=prev
Harry Brumer: fixed broken ISBN
2013-10-01T23:08:54Z
<p>fixed broken ISBN</p>
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Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=7507&oldid=prev
Harry Brumer: updated CAZyDBlink
2012-09-10T16:34:38Z
<p>updated CAZyDBlink</p>
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Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=6888&oldid=prev
Spencer Williams at 03:03, 14 June 2011
2011-06-14T03:03:03Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:03, 14 June 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28" >Line 28:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Substrate specificities ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Substrate specificities ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The overwhelming majority of [[glycoside hydrolase]]s of this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both [[endo]] and [[exo]] acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The overwhelming majority of [[glycoside hydrolase]]s of this family are polygalacturonases. They hydrolyse the <ins class="diffchange diffchange-inline">&</ins>alpha<ins class="diffchange diffchange-inline">;</ins>-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both [[endo]] and [[exo]] acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the <ins class="diffchange diffchange-inline">&</ins>alpha<ins class="diffchange diffchange-inline">;</ins>-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Kinetics and Mechanism ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Kinetics and Mechanism ==</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l34" >Line 34:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of rhamnogalacturonase revealed a cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the [[general acid]] residue (proton donor), whereas Asp180 (Asp202) and Asp202 (Asp224) are [[general base]]s that activate the nucleophilic water molecule (numbers are given for ''Aspergillus niger'' and in parantheses for ''Ewinia carotovora'' polygalacturonase).</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of rhamnogalacturonase revealed a cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in <ins class="diffchange diffchange-inline">&</ins>alpha<ins class="diffchange diffchange-inline">;</ins>-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with <ins class="diffchange diffchange-inline">&</ins>beta<ins class="diffchange diffchange-inline">;</ins>-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the [[general acid]] residue (proton donor), whereas Asp180 (Asp202) and Asp202 (Asp224) are [[general base]]s that activate the nucleophilic water molecule (numbers are given for ''Aspergillus niger'' and in parantheses for ''Ewinia carotovora'' polygalacturonase).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The structure of rhamnogalacturonase (RGase A) from ''Aspergillus aculeatus'' <cite>4</cite> revealed the signature parallel beta-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by having four, not three, parallel beta-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of beta-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from ''Yersinia enterocolitica'' shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The structure of rhamnogalacturonase (RGase A) from ''Aspergillus aculeatus'' <cite>4</cite> revealed the signature parallel <ins class="diffchange diffchange-inline">&</ins>beta<ins class="diffchange diffchange-inline">;</ins>-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by having four, not three, parallel <ins class="diffchange diffchange-inline">&</ins>beta<ins class="diffchange diffchange-inline">;</ins>-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of <ins class="diffchange diffchange-inline">&</ins>beta<ins class="diffchange diffchange-inline">;</ins>-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from ''Yersinia enterocolitica'' shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
</table>
Spencer Williams
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=5001&oldid=prev
Spencer Williams at 00:05, 20 June 2010
2010-06-20T00:05:48Z
<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<col class="diff-content" />
<tr class="diff-title" lang="en-CA">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 00:05, 20 June 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l34" >Line 34:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of rhamnogalacturonase revealed a cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the [[general acid]] residue (proton donor), whereas Asp180 (Asp202) and Asp202 (Asp224) activate the nucleophilic water molecule (numbers are given for ''Aspergillus niger'' and in parantheses for ''Ewinia carotovora'' polygalacturonase).</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of rhamnogalacturonase revealed a cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the [[general acid]] residue (proton donor), whereas Asp180 (Asp202) and Asp202 (Asp224) <ins class="diffchange diffchange-inline">are [[general base]]s that </ins>activate the nucleophilic water molecule (numbers are given for ''Aspergillus niger'' and in parantheses for ''Ewinia carotovora'' polygalacturonase).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l41" >Line 41:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First sterochemistry determination: Endopolygalacturonases from ''Aspergillus niger'' and ''Aspergillus tubingensis'' <cite>2</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First sterochemistry determination: Endopolygalacturonases from ''Aspergillus niger'' and ''Aspergillus tubingensis'' <cite>2</cite>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>;First [[general acid]] identification: ''Aspergillus niger'' endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor)<del class="diffchange diffchange-inline">, while </del>Asp180 (202) and Asp202 (224) active the nucleophilic water molecule (numbers are given for the ''Aspergillus niger'' and in parentheses for ''Erwinia carotovora'' polygalacturonase) <cite>6</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>;First [[general acid]] identification: ''Aspergillus niger'' endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor)<ins class="diffchange diffchange-inline">. Nnumbers are given for the ''Aspergillus niger'' and in parentheses for''Erwinia carotovora'' polygalacturonase) <cite>6</cite>.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">;First [[general base]] identification: ''Aspergillus niger'' endopolygalacturonase. </ins>Asp180 (202) and Asp202 (224) active the nucleophilic water molecule (numbers are given for the ''Aspergillus niger'' and in parentheses for ''Erwinia carotovora'' polygalacturonase) <cite>6</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First 3-D structure: Rhamnogalacturonase (RGase-A) from ''Aspergillus aculeatus'' <cite>4</cite>. First polygalacturonase structure, ''Erwinia carotovora'' polygalacturonase <cite>5</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First 3-D structure: Rhamnogalacturonase (RGase-A) from ''Aspergillus aculeatus'' <cite>4</cite>. First polygalacturonase structure, ''Erwinia carotovora'' polygalacturonase <cite>5</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.</div></td></tr>
</table>
Spencer Williams
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=5000&oldid=prev
Spencer Williams: /* Kinetics and Mechanism */
2010-06-19T23:54:13Z
<p><span dir="auto"><span class="autocomment">Kinetics and Mechanism</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:54, 19 June 2010</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Kinetics and Mechanism ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Kinetics and Mechanism ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Family GH28 enzymes follow an [[inverting]] mechanism; they harness a single displacement mechanism as revealed by <<del class="diffchange diffchange-inline">superscript</del>>1</<del class="diffchange diffchange-inline">superscript</del>>H-NMR spectroscopy of the products of hydrolysis in D<<del class="diffchange diffchange-inline">subscript</del>>2</<del class="diffchange diffchange-inline">subscript</del>>O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Family GH28 enzymes follow an [[inverting]] mechanism; they harness a single displacement mechanism as revealed by <<ins class="diffchange diffchange-inline">sup</ins>>1</<ins class="diffchange diffchange-inline">sup</ins>>H-NMR spectroscopy of the products of hydrolysis in D<<ins class="diffchange diffchange-inline">sub</ins>>2</<ins class="diffchange diffchange-inline">sub</ins>>O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td></tr>
</table>
Spencer Williams
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=4914&oldid=prev
Spencer Williams: /* Family Firsts */
2010-06-13T04:23:49Z
<p><span dir="auto"><span class="autocomment">Family Firsts</span></span></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en-CA">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:23, 13 June 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l41" >Line 41:</td>
<td colspan="2" class="diff-lineno">Line 41:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First sterochemistry determination: Endopolygalacturonases from ''Aspergillus niger'' and ''Aspergillus tubingensis'' <cite>2</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First sterochemistry determination: Endopolygalacturonases from ''Aspergillus niger'' and ''Aspergillus tubingensis'' <cite>2</cite>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>;First [[<del class="diffchange diffchange-inline">catalytic </del>acid]] identification: ''Aspergillus niger'' endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the nucleophilic water molecule (numbers are given for the ''Aspergillus niger'' and in parentheses for ''Erwinia carotovora'' polygalacturonase) <cite>6</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>;First [[<ins class="diffchange diffchange-inline">general </ins>acid]] identification: ''Aspergillus niger'' endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the nucleophilic water molecule (numbers are given for the ''Aspergillus niger'' and in parentheses for ''Erwinia carotovora'' polygalacturonase) <cite>6</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First 3-D structure: Rhamnogalacturonase (RGase-A) from ''Aspergillus aculeatus'' <cite>4</cite>. First polygalacturonase structure, ''Erwinia carotovora'' polygalacturonase <cite>5</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First 3-D structure: Rhamnogalacturonase (RGase-A) from ''Aspergillus aculeatus'' <cite>4</cite>. First polygalacturonase structure, ''Erwinia carotovora'' polygalacturonase <cite>5</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.</div></td></tr>
</table>
Spencer Williams
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_28&diff=4913&oldid=prev
Spencer Williams at 04:23, 13 June 2010
2010-06-13T04:23:29Z
<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en-CA">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:23, 13 June 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28" >Line 28:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Substrate specificities ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Substrate specificities ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The overwhelming majority of <del class="diffchange diffchange-inline">enzymes in </del>this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The overwhelming majority of <ins class="diffchange diffchange-inline">[[glycoside hydrolase]]s of </ins>this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both <ins class="diffchange diffchange-inline">[[</ins>endo<ins class="diffchange diffchange-inline">]] </ins>and <ins class="diffchange diffchange-inline">[[</ins>exo<ins class="diffchange diffchange-inline">]] </ins>acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Kinetics and Mechanism ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Kinetics and Mechanism ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Family GH28 enzymes <del class="diffchange diffchange-inline">are </del>inverting <del class="diffchange diffchange-inline">enzymes</del>; they harness a single displacement mechanism as revealed by <del class="diffchange diffchange-inline">1H</del>-NMR spectroscopy of the products of hydrolysis in <del class="diffchange diffchange-inline">D2O </del>reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Family GH28 enzymes <ins class="diffchange diffchange-inline">follow an [[</ins>inverting<ins class="diffchange diffchange-inline">]] mechanism</ins>; they harness a single displacement mechanism as revealed by <ins class="diffchange diffchange-inline"><superscript>1</superscript>H</ins>-NMR spectroscopy of the products of hydrolysis in <ins class="diffchange diffchange-inline">D<subscript>2</subscript>O </ins>reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Catalytic Residues ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of rhamnogalacturonase revealed <del class="diffchange diffchange-inline">the </del>cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), <del class="diffchange diffchange-inline">while </del>Asp180 (Asp202) and Asp202 (Asp224) <del class="diffchange diffchange-inline">active </del>the <del class="diffchange diffchange-inline">catalytic </del>water molecule (numbers are given for ''Aspergillus niger'' and in parantheses for ''Ewinia carotovora'' polygalacturonase).</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of rhamnogalacturonase revealed <ins class="diffchange diffchange-inline">a </ins>cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the <ins class="diffchange diffchange-inline">[[</ins>general acid<ins class="diffchange diffchange-inline">]] residue </ins>(proton donor), <ins class="diffchange diffchange-inline">whereas </ins>Asp180 (Asp202) and Asp202 (Asp224) <ins class="diffchange diffchange-inline">activate </ins>the <ins class="diffchange diffchange-inline">nucleophilic </ins>water molecule (numbers are given for ''Aspergillus niger'' and in parantheses for ''Ewinia carotovora'' polygalacturonase).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Three-dimensional structures ==</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l41" >Line 41:</td>
<td colspan="2" class="diff-lineno">Line 41:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First sterochemistry determination: Endopolygalacturonases from ''Aspergillus niger'' and ''Aspergillus tubingensis'' <cite>2</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First sterochemistry determination: Endopolygalacturonases from ''Aspergillus niger'' and ''Aspergillus tubingensis'' <cite>2</cite>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>;First [[catalytic acid]] identification: ''Aspergillus niger'' endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the <del class="diffchange diffchange-inline">catalytic </del>water molecule (numbers are given for the ''Aspergillus niger'' and in parentheses for ''Erwinia carotovora'' polygalacturonase) <cite>6</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>;First [[catalytic acid]] identification: ''Aspergillus niger'' endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the <ins class="diffchange diffchange-inline">nucleophilic </ins>water molecule (numbers are given for the ''Aspergillus niger'' and in parentheses for ''Erwinia carotovora'' polygalacturonase) <cite>6</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First 3-D structure: Rhamnogalacturonase (RGase-A) from ''Aspergillus aculeatus'' <cite>4</cite>. First polygalacturonase structure, ''Erwinia carotovora'' polygalacturonase <cite>5</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First 3-D structure: Rhamnogalacturonase (RGase-A) from ''Aspergillus aculeatus'' <cite>4</cite>. First polygalacturonase structure, ''Erwinia carotovora'' polygalacturonase <cite>5</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.</div></td></tr>
</table>
Spencer Williams