View source for 8bqa


==CjCel5B endo-glucanase bound to CB665 covalent inhibitor==
<StructureSection load='8bqa' size='340' side='right'caption='[[8bqa]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8bqa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQA 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]] 1.67&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RBH:~{N}-[(2~{S},3~{S},4~{S},5~{R})-2-(hydroxymethyl)-4,5,6-tris(oxidanyl)oxan-3-yl]-2-oxidanyl-ethanamide'>RBH</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>, <scene name='pdbligand=YLL:(1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL'>YLL</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=8bqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqa OCA], [https://pdbe.org/8bqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqa RCSB], [https://www.ebi.ac.uk/pdbsum/8bqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqa ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacteria and yeasts grow on biomass polysaccharides by expressing and excreting a complex array of glycoside hydrolase (GH) enzymes. Identification and annotation of such GH pools, which are valuable commodities for sustainable energy and chemistries, by conventional means (genomics, proteomics) are complicated, as primary sequence or secondary structure alignment with known active enzymes is not always predictive for new ones. Here we report a "low-tech", easy-to-use, and sensitive multiplexing activity-based protein-profiling platform to characterize the xyloglucan-degrading GH system excreted by the soil saprophyte, Cellvibrio japonicus, when grown on xyloglucan. A suite of activity-based probes bearing orthogonal fluorophores allows for the visualization of accessory exo-acting glycosidases, which are then identified using biotin-bearing probes. Substrate specificity of xyloglucanases is directly revealed by imbuing xyloglucan structural elements into bespoke activity-based probes. Our ABPP platform provides a highly useful tool to dissect xyloglucan-degrading systems from various sources and to rapidly select potentially useful ones. The observed specificity of the probes moreover bodes well for the study of other biomass polysaccharide-degrading systems, by modeling probe structures to those of desired substrates.

A Multiplexing Activity-Based Protein-Profiling Platform for Dissection of a Native Bacterial Xyloglucan-Degrading System.,McGregor NGS, de Boer C, Foucart QPO, Beenakker T, Offen WA, Codee JDC, Willems LI, Overkleeft HS, Davies GJ ACS Cent Sci. 2023 Nov 24;9(12):2306-2314. doi: 10.1021/acscentsci.3c00831. , eCollection 2023 Dec 27. PMID:38161374<ref>PMID:38161374</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8bqa" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Cellvibrio japonicus]]
[[Category: Large Structures]]
[[Category: Davies GJ]]
[[Category: McGregor NGS]]
[[Category: Overkleeft HS]]
[[Category: De Boer C]]