3wlm: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 3wlm is ~~ON HOLD~~

==Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme exo1 in complex with octyl-O-glucoside==

== Structural highlights ==

<table><tr><td colspan='2'>[[3wlm]] 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=3WLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WLM 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]] 1.9Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=3wlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wlm OCA], [https://pdbe.org/3wlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wlm RCSB], [https://www.ebi.ac.uk/pdbsum/3wlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wlm ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Q9XEI3_HORVV Q9XEI3_HORVV]

== Publication Abstract from PubMed ==

Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl beta-D-glucoside and methyl 6-thio-beta-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-beta-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.

~~Authors:~~ Streltsov, V.A., Hrmova, M.

Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.,Streltsov VA, Luang S, Peisley A, Varghese JN, Ketudat Cairns JR, Fort S, Hijnen M, Tvaroska I, Arda A, Jimenez-Barbero J, Alfonso-Prieto M, Rovira C, Mendoza F, Tiessler-Sala L, Sanchez-Aparicio JE, Rodriguez-Guerra J, Lluch JM, Marechal JD, Masgrau L, Hrmova M Nat Commun. 2019 May 20;10(1):2222. doi: 10.1038/s41467-019-09691-z. PMID:31110237<ref>PMID:31110237</ref>

~~Description: CRYSTAL STRUCTURE OF BARLEY BETA~~-D-~~GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 IN COMPLEX WITH OCTYL-O-GLUCOSIDE~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Hordeum vulgare subsp. vulgare]]

[[Category: Large Structures]]

[[Category: Hrmova M]]

[[Category: Streltsov VA]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 3wlm is ON HOLD
+==Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme exo1 in complex with octyl-O-glucoside==
+<StructureSection load='3wlm' size='340' side='right'caption='[[3wlm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3wlm]] 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=3WLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WLM 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=3wlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wlm OCA], [https://pdbe.org/3wlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wlm RCSB], [https://www.ebi.ac.uk/pdbsum/3wlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wlm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9XEI3_HORVV Q9XEI3_HORVV]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl beta-D-glucoside and methyl 6-thio-beta-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-beta-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.
-Authors: Streltsov, V.A., Hrmova, M.
+Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.,Streltsov VA, Luang S, Peisley A, Varghese JN, Ketudat Cairns JR, Fort S, Hijnen M, Tvaroska I, Arda A, Jimenez-Barbero J, Alfonso-Prieto M, Rovira C, Mendoza F, Tiessler-Sala L, Sanchez-Aparicio JE, Rodriguez-Guerra J, Lluch JM, Marechal JD, Masgrau L, Hrmova M Nat Commun. 2019 May 20;10(1):2222. doi: 10.1038/s41467-019-09691-z. PMID:31110237<ref>PMID:31110237</ref>
-Description: CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 IN COMPLEX WITH OCTYL-O-GLUCOSIDE
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3wlm" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Hordeum vulgare subsp. vulgare]]
+[[Category: Large Structures]]
+[[Category: Hrmova M]]
+[[Category: Streltsov VA]]