https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&feed=atom&action=history
Glycoside Hydrolase Family 144 - Revision history
2024-03-28T19:44:05Z
Revision history for this page on the wiki
MediaWiki 1.35.10
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=17779&oldid=prev
Masahiro Nakajima at 05:06, 2 February 2024
2024-02-02T05:06:51Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 05:06, 2 February 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l42" >Line 42:</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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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="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 unliganded crystal structures of [[GH144]] enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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 unliganded crystal structures of [[GH144]] enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized<ins class="diffchange diffchange-inline">. Later, [[GH144]] is classified into clan GH-S with [[GH162]] based on structural similarity between them <cite>Tanaka2024</cite></ins>. </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>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l55" >Line 55:</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>#Shimizu2018 pmid=29763309</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>#Shimizu2018 pmid=29763309</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>#Tanaka2019 pmid=30926603</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>#Tanaka2019 pmid=30926603</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 style="font-weight: bold; text-decoration: none;">#Tanaka2024 pmid=38300345</ins></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></biblio></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></biblio></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;"></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>[[Category:Glycoside Hydrolase Families|GH144]]</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>[[Category:Glycoside Hydrolase Families|GH144]]</div></td></tr>
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Masahiro Nakajima
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=17778&oldid=prev
Masahiro Nakajima at 05:02, 2 February 2024
2024-02-02T05:02:53Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 05:02, 2 February 2024</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>|'''Clan''' </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>|'''Clan''' </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>|<del class="diffchange diffchange-inline">None</del></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>|<ins class="diffchange diffchange-inline">GH-S</ins></div></td></tr>
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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>|'''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>|'''Mechanism'''</div></td></tr>
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Masahiro Nakajima
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=16507&oldid=prev
Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"
2021-12-18T21:14:59Z
<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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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:14, 18 December 2021</td>
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<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>* [[Author]]: <del class="diffchange diffchange-inline">^^^</del>Koichi Abe<del class="diffchange diffchange-inline">^^^</del></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>* [[Author]]: <ins class="diffchange diffchange-inline">[[User:</ins>Koichi Abe<ins class="diffchange diffchange-inline">|Koichi Abe]]</ins></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>* [[Responsible Curator]]: <del class="diffchange diffchange-inline">^^^</del>Masahiro Nakajima<del class="diffchange diffchange-inline">^^^</del></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>* [[Responsible Curator]]: <ins class="diffchange diffchange-inline">[[User:</ins>Masahiro Nakajima<ins class="diffchange diffchange-inline">|Masahiro Nakajima]]</ins></div></td></tr>
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Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=14319&oldid=prev
Masahiro Nakajima at 00:10, 16 October 2019
2019-10-16T00:10:39Z
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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>* [[Author]]: ^^^Koichi Abe^^^</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>* [[Author]]: ^^^Koichi Abe^^^</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>* [[Responsible Curator]]: ^^^Masahiro Nakajima^^^</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>* [[Responsible Curator]]: ^^^Masahiro Nakajima^^^</div></td></tr>
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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>[[Glycoside hydrolase]] family [[<del class="diffchange diffchange-inline">144</del>]] contains β-1,2-glucan-hydrolyzing enzymes. The first characterized enzymes of this family are an ''endo''-β-1,2-glucanase ([{{EClink}}3.2.1.71 EC 3.2.1.71]) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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>[[Glycoside hydrolase]] family <ins class="diffchange diffchange-inline">144 (</ins>[[<ins class="diffchange diffchange-inline">GH144</ins>]]<ins class="diffchange diffchange-inline">) </ins>contains β-1,2-glucan-hydrolyzing enzymes. The first characterized enzymes of this family are an ''endo''-β-1,2-glucanase ([{{EClink}}3.2.1.71 EC 3.2.1.71]) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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-l35" >Line 35:</td>
<td colspan="2" class="diff-lineno">Line 35:</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>Mutational analysis of CpSGL indicated that Asp139, Glu142, and Glu211 play important roles in catalysis <cite>Abe2017</cite>. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of the glucose moieties in sophorotriose, nor are they proximal to the space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold ([[GH8]], [[GH15]], and [[GH162]]) did not provide clues to the assignment of the catalytic residues. These observation may imply that GH144 enzymes have a non-canonical reaction mechanism.</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>Mutational analysis of CpSGL indicated that Asp139, Glu142, and Glu211 play important roles in catalysis <cite>Abe2017</cite>. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of the glucose moieties in sophorotriose, nor are they proximal to the space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold ([[GH8]], [[GH15]], and [[GH162]]) did not provide clues to the assignment of the catalytic residues. These observation may imply that <ins class="diffchange diffchange-inline">[[</ins>GH144<ins class="diffchange diffchange-inline">]] </ins>enzymes have a non-canonical reaction mechanism.</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-l42" >Line 42:</td>
<td colspan="2" class="diff-lineno">Line 42:</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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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="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 unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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 unliganded crystal structures of <ins class="diffchange diffchange-inline">[[</ins>GH144<ins class="diffchange diffchange-inline">]] </ins>enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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>
Masahiro Nakajima
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=14318&oldid=prev
Masahiro Nakajima at 00:04, 16 October 2019
2019-10-16T00:04:18Z
<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 00:04, 16 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l29" >Line 29:</td>
<td colspan="2" class="diff-lineno">Line 29:</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>== 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>[[Glycoside hydrolase]] family 144 contains β-1,2-glucan-hydrolyzing enzymes. The first characterized enzymes of this family are an ''endo''-β-1,2-glucanase ([{{EClink}}3.2.1.71 EC 3.2.1.71]) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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>[[Glycoside hydrolase]] family <ins class="diffchange diffchange-inline">[[</ins>144<ins class="diffchange diffchange-inline">]] </ins>contains β-1,2-glucan-hydrolyzing enzymes. The first characterized enzymes of this family are an ''endo''-β-1,2-glucanase ([{{EClink}}3.2.1.71 EC 3.2.1.71]) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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>
</table>
Masahiro Nakajima
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=14317&oldid=prev
Harry Brumer: Removed unpublished data reference, according to CAZypedia policy
2019-10-15T23:27:24Z
<p>Removed unpublished data reference, according to CAZypedia policy</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 23:27, 15 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l40" >Line 40:</td>
<td colspan="2" class="diff-lineno">Line 40:</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>The 3-D structures of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]) and BDI_3064 (PDB ID [{{PDBlink}}5z06 5Z06]) were determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of [[GH162]] ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</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>The 3-D structures of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]) and BDI_3064 (PDB ID [{{PDBlink}}5z06 5Z06]) were determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of [[GH162]] ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</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="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 CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively<del class="diffchange diffchange-inline">. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data)</del>. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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 CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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>The unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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>The unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</div></td></tr>
</table>
Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=14316&oldid=prev
Harry Brumer: minor language edits
2019-10-15T23:26:32Z
<p>minor language edits</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 23:26, 15 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l38" >Line 38:</td>
<td colspan="2" class="diff-lineno">Line 38:</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 3-D structures of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]) and BDI_3064 (PDB ID [{{PDBlink}}5z06 5Z06]) were determined by X-ray crystallography and <del class="diffchange diffchange-inline">showed an </del>(α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of GH162 ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</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 3-D structures of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]) and BDI_3064 (PDB ID [{{PDBlink}}5z06 5Z06]) were determined by X-ray crystallography and <ins class="diffchange diffchange-inline">revealed the </ins>(α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of <ins class="diffchange diffchange-inline">[[</ins>GH162<ins class="diffchange diffchange-inline">]] </ins>''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data). The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the <del class="diffchange diffchange-inline">nonreducing </del>end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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> </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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data). The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the <ins class="diffchange diffchange-inline">non-reducing </ins>end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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> </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>The unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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>The unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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 colspan="2" class="diff-lineno" id="mw-diff-left-l46" >Line 46:</td>
<td colspan="2" class="diff-lineno">Line 48:</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 general acid residue identification: Not known.</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 general acid residue identification: Not known.</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 general base residue identification: Not known.</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 general base residue identification: Not known.</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 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 (PDB ID [{{PDBlink}}3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species (PDB IDs [{{PDBlink}}4gl3 4GL3] and [{{PDBlink}}4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there <del class="diffchange diffchange-inline">is </del>no <del class="diffchange diffchange-inline">publication about </del>these proteins. The first published structures are those of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]), one of which ([{{PDBlink}}5gzh 5GZH]) captures sophorotriose and glucose.</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 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 (PDB ID [{{PDBlink}}3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species (PDB IDs [{{PDBlink}}4gl3 4GL3] and [{{PDBlink}}4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there <ins class="diffchange diffchange-inline">are </ins>no <ins class="diffchange diffchange-inline">journal publications describing </ins>these proteins. The first published structures are those of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]), one of which ([{{PDBlink}}5gzh 5GZH]) captures sophorotriose and glucose.</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>== References ==</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>== References ==</div></td></tr>
</table>
Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=14315&oldid=prev
Harry Brumer: standardized PDB links
2019-10-15T23:23:21Z
<p>standardized PDB links</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 23:23, 15 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l38" >Line 38:</td>
<td colspan="2" class="diff-lineno">Line 38:</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 3-D structures of CpSGL ([<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>5gzh 5GZH] and [<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>5gzk 5GZK]) and BDI_3064 ([<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>5z06 5Z06]) were determined by X-ray crystallography and showed an (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of GH162 ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</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 3-D structures of CpSGL (<ins class="diffchange diffchange-inline">PDB IDs </ins>[<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>5gzh 5GZH] and [<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>5gzk 5GZK]) and BDI_3064 (<ins class="diffchange diffchange-inline">PDB ID </ins>[<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>5z06 5Z06]) were determined by X-ray crystallography and showed an (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of GH162 ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data). The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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>The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data). The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.</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 unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species ([<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>3eu8 3EU8], [<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>4gl3 4GL3], and [<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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 unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (<ins class="diffchange diffchange-inline">PDB IDs </ins>[<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>3eu8 3EU8], [<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>4gl3 4GL3], and [<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l46" >Line 46:</td>
<td colspan="2" class="diff-lineno">Line 46:</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 general acid residue identification: Not known.</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 general acid residue identification: Not known.</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 general base residue identification: Not known.</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 general base residue identification: Not known.</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 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 ([<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species ([<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>4gl3 4GL3] and [<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there is no publication about these proteins. The first published structures are those of CpSGL ([<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>5gzh 5GZH] and [<del class="diffchange diffchange-inline">https://www.rcsb.org/structure/</del>5gzk 5GZK]), one of which (<del class="diffchange diffchange-inline">5GZK</del>) captures sophorotriose and glucose.</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 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 (<ins class="diffchange diffchange-inline">PDB ID </ins>[<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species (<ins class="diffchange diffchange-inline">PDB IDs </ins>[<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>4gl3 4GL3] and [<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there is no publication about these proteins. The first published structures are those of CpSGL (<ins class="diffchange diffchange-inline">PDB IDs </ins>[<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>5gzh 5GZH] and [<ins class="diffchange diffchange-inline">{{PDBlink}}</ins>5gzk 5GZK]), one of which (<ins class="diffchange diffchange-inline">[{{PDBlink}}5gzh 5GZH]</ins>) captures sophorotriose and glucose.</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>== References ==</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>== References ==</div></td></tr>
</table>
Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=14314&oldid=prev
Harry Brumer: minor language edits
2019-10-15T23:19:53Z
<p>minor language edits</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 23:19, 15 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l29" >Line 29:</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>[[Glycoside hydrolase]] family 144 contains β-1,2-glucan-hydrolyzing enzymes. The characterized enzymes of this family are an ''endo''-β-1,2-glucanase (EC 3.2.1.71) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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>[[Glycoside hydrolase]] family 144 contains β-1,2-glucan-hydrolyzing enzymes. The <ins class="diffchange diffchange-inline">first </ins>characterized enzymes of this family are an ''endo''-β-1,2-glucanase (<ins class="diffchange diffchange-inline">[{{EClink}}3.2.1.71 </ins>EC 3.2.1.71<ins class="diffchange diffchange-inline">]</ins>) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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>CpSGL hydrolyzes cyclic β-1,2-glucan, showing that this enzyme is ''endo''-<del class="diffchange diffchange-inline">lytic</del>, whereas BDI_3064 does not, indicating that this enzyme is ''exo''-<del class="diffchange diffchange-inline">lytic </del><cite>Abe2017, Shimizu2018</cite>. Monitoring the stereochemical course of the hydrolysis of β-1,2-glucan by <sup>1</sup>H-NMR showed that CpSGL <del class="diffchange diffchange-inline">use </del>an inverting mechanism to hydrolyze β-1,2-glucan <cite>Abe2017</cite>. Monitoring the change of the degree of optical rotation during hydrolysis of β-1,2-glucan by CpSGL also supported this mechanism <cite>Abe2017</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>CpSGL hydrolyzes cyclic β-1,2-glucan, showing that this enzyme is ''endo''-<ins class="diffchange diffchange-inline">hydrolytic</ins>, whereas BDI_3064 does not, indicating that this enzyme is ''exo''-<ins class="diffchange diffchange-inline">hydrolytic </ins><cite>Abe2017, Shimizu2018</cite>. Monitoring the stereochemical course of the hydrolysis of β-1,2-glucan by <sup>1</sup>H-NMR showed that CpSGL <ins class="diffchange diffchange-inline">uses </ins>an inverting mechanism to hydrolyze β-1,2-glucan <cite>Abe2017</cite>. Monitoring the change of the degree of optical rotation during hydrolysis of β-1,2-glucan by CpSGL also supported this mechanism <cite>Abe2017</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>Mutational analysis of CpSGL indicated that Asp139, Glu142, and Glu211 play important roles in catalysis <cite>Abe2017</cite>. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of <del class="diffchange diffchange-inline">all </del>the glucose moieties in sophorotriose <del class="diffchange diffchange-inline">or </del>are proximal to space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold (GH8, GH15, and GH162) did not provide clues to the assignment of the catalytic residues. These observation may imply that GH144 enzymes have a non-canonical reaction mechanism.</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>Mutational analysis of CpSGL indicated that Asp139, Glu142, and Glu211 play important roles in catalysis <cite>Abe2017</cite>. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of the glucose moieties in sophorotriose<ins class="diffchange diffchange-inline">, nor </ins>are <ins class="diffchange diffchange-inline">they </ins>proximal to <ins class="diffchange diffchange-inline">the </ins>space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold (<ins class="diffchange diffchange-inline">[[</ins>GH8<ins class="diffchange diffchange-inline">]]</ins>, <ins class="diffchange diffchange-inline">[[</ins>GH15<ins class="diffchange diffchange-inline">]]</ins>, and <ins class="diffchange diffchange-inline">[[</ins>GH162<ins class="diffchange diffchange-inline">]]</ins>) did not provide clues to the assignment of the catalytic residues. These observation may imply that GH144 enzymes have a non-canonical reaction mechanism.</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>
</table>
Harry Brumer
https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_144&diff=14302&oldid=prev
Koichi Abe at 10:54, 14 October 2019
2019-10-14T10:54:26Z
<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 10:54, 14 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l29" >Line 29:</td>
<td colspan="2" class="diff-lineno">Line 29:</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>== 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>[[Glycoside hydrolase]] family 144 contains β-1,2-glucan-hydrolyzing enzymes. The characterized enzymes of this family are an ''endo''-β-1,2-glucanase (EC 3.2.1.71) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) <del class="diffchange diffchange-inline">form </del>the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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>[[Glycoside hydrolase]] family 144 contains β-1,2-glucan-hydrolyzing enzymes. The characterized enzymes of this family are an ''endo''-β-1,2-glucanase (EC 3.2.1.71) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064) <cite>Abe2017<ins class="diffchange diffchange-inline">, Shimizu2018</ins></cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) <ins class="diffchange diffchange-inline">from </ins>the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.</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>CpSGL hydrolyzes cyclic β-1,2-glucan, showing that this enzyme is ''endo''-lytic, whereas BDI_3064 does not, indicating that this enzyme is ''exo''-lytic. Monitoring stereochemical course of the hydrolysis of β-1,2-glucan by <sup>1</sup>H-NMR showed that CpSGL use an inverting mechanism to hydrolyze β-1,2-glucan. Monitoring the change of the degree of optical rotation during hydrolysis of β-1,2-glucan by CpSGL also supported this mechanism.</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>CpSGL hydrolyzes cyclic β-1,2-glucan, showing that this enzyme is ''endo''-lytic, whereas BDI_3064 does not, indicating that this enzyme is ''exo''-lytic <ins class="diffchange diffchange-inline"><cite>Abe2017, Shimizu2018</cite></ins>. Monitoring <ins class="diffchange diffchange-inline">the </ins>stereochemical course of the hydrolysis of β-1,2-glucan by <sup>1</sup>H-NMR showed that CpSGL use an inverting mechanism to hydrolyze β-1,2-glucan <ins class="diffchange diffchange-inline"><cite>Abe2017</cite></ins>. Monitoring the change of the degree of optical rotation during hydrolysis of β-1,2-glucan by CpSGL also supported this mechanism <ins class="diffchange diffchange-inline"><cite>Abe2017</cite></ins>.</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>Mutational analysis of CpSGL indicated that Asp139, Glu142 and Glu211 play important roles in catalysis. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of all the glucose moieties in sophorotriose or are proximal to space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold (GH8, GH15 and GH162) did not provide clues to the assignment of the catalytic residues. These observation may imply that GH144 enzymes have a non-canonical reaction mechanism.</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>Mutational analysis of CpSGL indicated that Asp139, Glu142<ins class="diffchange diffchange-inline">, </ins>and Glu211 play important roles in catalysis <ins class="diffchange diffchange-inline"><cite>Abe2017</cite></ins>. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of all the glucose moieties in sophorotriose or are proximal to space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold (GH8, GH15<ins class="diffchange diffchange-inline">, </ins>and GH162) did not provide clues to the assignment of the catalytic residues. These observation may imply that GH144 enzymes have a non-canonical reaction mechanism.</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 3-D structures of CpSGL ([https://www.rcsb.org/structure/5gzh 5GZH] and [https://www.rcsb.org/structure/5gzk 5GZK]) and BDI_3064 ([https://www.rcsb.org/structure/5z06 5Z06]) were determined by X-ray crystallography and showed an (α/α)<sub>6</sub>-fold of this family. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme as described below. The overall structure of CpSGL is similar to that of GH162 ''endo''-β-1,2-glucanase (TfSGL).</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 3-D structures of CpSGL ([https://www.rcsb.org/structure/5gzh 5GZH] and [https://www.rcsb.org/structure/5gzk 5GZK]) and BDI_3064 ([https://www.rcsb.org/structure/5z06 5Z06]) were determined by X-ray crystallography and showed an (α/α)<sub>6</sub>-fold of this family <ins class="diffchange diffchange-inline"><cite>Abe2017</cite></ins>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme<ins class="diffchange diffchange-inline">, </ins>as described below. The overall structure of CpSGL is similar to that of GH162 ''endo''-β-1,2-glucanase (TfSGL) <ins class="diffchange diffchange-inline">despite their low sequence similarity <cite>Tanaka2019</cite></ins>.</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 CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS <del class="diffchange diffchange-inline">analyses </del>suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharides. This structural feature <del class="diffchange diffchange-inline">makes </del>BDI_3064 an ''exo''-acting enzyme.</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 CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS <ins class="diffchange diffchange-inline">analysis </ins>suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment <ins class="diffchange diffchange-inline">(unpublished data)</ins>. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharides <ins class="diffchange diffchange-inline"><cite>Shimizu2018</cite></ins>. This structural feature <ins class="diffchange diffchange-inline">would make </ins>BDI_3064 an ''exo''-acting enzyme.</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 unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species ([https://www.rcsb.org/structure/3eu8 3EU8], [https://www.rcsb.org/structure/4gl3 4GL3] and [https://www.rcsb.org/structure/4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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 unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species ([https://www.rcsb.org/structure/3eu8 3EU8], [https://www.rcsb.org/structure/4gl3 4GL3]<ins class="diffchange diffchange-inline">, </ins>and [https://www.rcsb.org/structure/4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.</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>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l51" >Line 51:</td>
<td colspan="2" class="diff-lineno">Line 51:</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><biblio></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><biblio></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>#Abe2017 pmid=28270506</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>#Abe2017 pmid=28270506</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> </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><ins class="diffchange diffchange-inline">#Shimizu2018 pmid=29763309</ins></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> </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>#<ins class="diffchange diffchange-inline">Tanaka2019 pmid=30926603</ins></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>#<del class="diffchange diffchange-inline">DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].</del></div></td><td colspan="2"> </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></biblio></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></biblio></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;"></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>[[Category:Glycoside Hydrolase Families|GH144]]</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>[[Category:Glycoside Hydrolase Families|GH144]]</div></td></tr>
</table>
Koichi Abe