6sxt
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==GH54 a-l-arabinofuranosidase soaked with aziridine inhibitor== | |
| + | <StructureSection load='6sxt' size='340' side='right'caption='[[6sxt]], [[Resolution|resolution]] 1.47Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6sxt]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SXT FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LXE:[(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl]azanium'>LXE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6sxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sxt OCA], [http://pdbe.org/6sxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sxt RCSB], [http://www.ebi.ac.uk/pdbsum/6sxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sxt ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[http://www.uniprot.org/uniprot/ABFB_ASPKW ABFB_ASPKW]] Alpha-L-arabinofuranosidase involved in the degradation of arabinoxylan, a major component of plant hemicellulose. Able to hydrolyze 1,5-, 1,3- and 1,2-alpha-linkages not only in L-arabinofuranosyl oligosaccharides, but also in polysaccharides containing terminal non-reducing L-arabinofuranoses in side chains, like L-arabinan, arabinogalactan and arabinoxylan.<ref>PMID:15292273</ref> <ref>PMID:16233515</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 6sxt" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Non-reducing end alpha-L-arabinofuranosidase]] | ||
| + | [[Category: Davies, G J]] | ||
| + | [[Category: McGregor, N G.S]] | ||
| + | [[Category: Nin-Hill, A]] | ||
| + | [[Category: Rovira, C]] | ||
| + | [[Category: Arabinofuranosidase]] | ||
| + | [[Category: Aspergillus]] | ||
| + | [[Category: Covalent complex]] | ||
| + | [[Category: Gh54]] | ||
| + | [[Category: Hydrolase]] | ||
Revision as of 09:23, 26 February 2020
GH54 a-l-arabinofuranosidase soaked with aziridine inhibitor
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