View source for 6sxs


==GH54 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor==
<StructureSection load='6sxs' size='340' side='right'caption='[[6sxs]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6sxs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_luchuensis Aspergillus luchuensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SXS 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]] 1.859&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6sxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sxs OCA], [https://pdbe.org/6sxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sxs RCSB], [https://www.ebi.ac.uk/pdbsum/6sxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sxs ProSAT]</span></td></tr>
</table>
== Function ==
[https://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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6sxs" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aspergillus luchuensis]]
[[Category: Large Structures]]
[[Category: Davies GJ]]
[[Category: McGregor NGS]]
[[Category: Nin-Hill A]]
[[Category: Rovira C]]