8bqb: Difference between revisions
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==CjCel5C endo-glucanase bound to CB396 covalent inhibitor== | |||
<StructureSection load='8bqb' size='340' side='right'caption='[[8bqb]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8bqb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus_Ueda107 Cellvibrio japonicus Ueda107]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQB 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]] 2.701Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</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=8bqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqb OCA], [https://pdbe.org/8bqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqb RCSB], [https://www.ebi.ac.uk/pdbsum/8bqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqb ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/B3PF55_CELJU B3PF55_CELJU] | |||
<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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8bqb" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Cellvibrio japonicus Ueda107]] | |||
[[Category: Large Structures]] | |||
[[Category: Davies GJ]] | |||
[[Category: McGregor NGS]] | |||
[[Category: Overkleeft HS]] | |||
[[Category: De Boer C]] | |||
Latest revision as of 08:17, 12 June 2024
CjCel5C endo-glucanase bound to CB396 covalent inhibitorCjCel5C endo-glucanase bound to CB396 covalent inhibitor
Structural highlights
FunctionPublication Abstract from PubMedBacteria 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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