6sxu
From Proteopedia
(Difference between revisions)
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==GH51 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor== | |
| + | <StructureSection load='6sxu' size='340' side='right'caption='[[6sxu]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6sxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SXU 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]] 1.398Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LX5:[(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl]+hydrogen+sulfate'>LX5</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6sxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sxu OCA], [https://pdbe.org/6sxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sxu RCSB], [https://www.ebi.ac.uk/pdbsum/6sxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sxu ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/IABF_GEOSE IABF_GEOSE] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref> <ref>PMID:7887599</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Identifying and characterizing the enzymes responsible for an observed activity within a complex eukaryotic catabolic system remains one of the most significant challenges in the study of biomass-degrading systems. The debranching of both complex hemicellulosic and pectinaceous polysaccharides requires the production of alpha-L-arabinofuranosidases among a wide variety of co-expressed carbohydrate-active enzymes. To selectively detect and identify alpha-L-arabinofuranosidases produced by fungi grown on complex biomass, potential covalent inhibitors and probes which mimic alpha-L-arabinofuranosides were sought. The conformational free energy landscapes of free alpha-L-arabinofuranose and several rationally designed covalent alpha-L-arabinofuranosidase inhibitors were analyzed. A synthetic route to these inhibitors was subsequently developed based on a key Wittig-Still rearrangement. Through a combination of kinetic measurements, intact mass spectrometry, and structural experiments, the designed inhibitors were shown to efficiently label the catalytic nucleophiles of retaining GH51 and GH54 alpha-L-arabinofuranosidases. Activity-based probes elaborated from an inhibitor with an aziridine warhead were applied to the identification and characterization of alpha-L-arabinofuranosidases within the secretome of A. niger grown on arabinan. This method was extended to the detection and identification of alpha-L-arabinofuranosidases produced by eight biomass-degrading basidiomycete fungi grown on complex biomass. The broad applicability of the cyclophellitol-derived activity-based probes and inhibitors presented here make them a valuable new tool in the characterization of complex eukaryotic carbohydrate-degrading systems and in the high-throughput discovery of alpha-L-arabinofuranosidases. | ||
| - | + | Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-L-Arabinofuranosidases.,McGregor N, Artola M, Nin-Hill A, Linzel D, Haon M, Reijngoud J, Ram AFJ, Rosso MN, van der Marel GA, Codee JDC, van Wezel GP, Berrin JG, Rovira C, Overkleeft HS, Davies GJ J Am Chem Soc. 2020 Feb 13. doi: 10.1021/jacs.9b11351. PMID:32053363<ref>PMID:32053363</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 6sxu" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Geobacillus stearothermophilus]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Davies GJ]] | ||
| + | [[Category: McGregor NGS]] | ||
Current revision
GH51 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor
| |||||||||||
