6k6v: Difference between revisions

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<StructureSection load='6k6v' size='340' side='right'caption='[[6k6v]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
<StructureSection load='6k6v' size='340' side='right'caption='[[6k6v]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6k6v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare_subsp._vulgare Hordeum vulgare subsp. vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K6V FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K6V FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900098:METHYL+6-THIO-BETA-GENTIOBIOSIDE'>PRD_900098</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U1Y:methyl+6-thio-beta-D-glucopyranoside'>U1Y</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900098:METHYL+6-THIO-BETA-GENTIOBIOSIDE'>PRD_900098</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U1Y:methyl+6-thio-beta-D-glucopyranoside'>U1Y</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k6v OCA], [https://pdbe.org/6k6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k6v RCSB], [https://www.ebi.ac.uk/pdbsum/6k6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k6v ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k6v OCA], [https://pdbe.org/6k6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k6v RCSB], [https://www.ebi.ac.uk/pdbsum/6k6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k6v ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9XEI3_HORVV Q9XEI3_HORVV]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In the barley beta-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures beta-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric beta-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-beta-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.
The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases.,Luang S, Fernandez-Luengo X, Nin-Hill A, Streltsov VA, Schwerdt JG, Alonso-Gil S, Ketudat Cairns JR, Pradeau S, Fort S, Marechal JD, Masgrau L, Rovira C, Hrmova M Nat Commun. 2022 Sep 23;13(1):5577. doi: 10.1038/s41467-022-33180-5. PMID:36151080<ref>PMID:36151080</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6k6v" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Hordeum vulgare subsp. vulgare]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hrmova M]]
[[Category: Hrmova M]]
[[Category: Luang S]]
[[Category: Luang S]]
[[Category: Streltsov VA]]
[[Category: Streltsov VA]]
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