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| | <StructureSection load='6sxt' size='340' side='right'caption='[[6sxt]], [[Resolution|resolution]] 1.47Å' scene=''> | | <StructureSection load='6sxt' size='340' side='right'caption='[[6sxt]], [[Resolution|resolution]] 1.47Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6sxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspkw Aspkw]. 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> | + | <table><tr><td colspan='2'>[[6sxt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_luchuensis_IFO_4308 Aspergillus luchuensis IFO 4308]. 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 [https://proteopedia.org/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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.466Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">abfB, AKAW_08685 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1033177 ASPKW])</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=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'>[https://proteopedia.org/fgij/fg.htm?mol=6sxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sxt OCA], [https://pdbe.org/6sxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sxt RCSB], [https://www.ebi.ac.uk/pdbsum/6sxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sxt ProSAT]</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> | | </table> |
| | == Function == | | == 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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aspkw]] | + | [[Category: Aspergillus luchuensis IFO 4308]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Non-reducing end alpha-L-arabinofuranosidase]]
| + | [[Category: Davies GJ]] |
| - | [[Category: Davies, G J]] | + | [[Category: McGregor NGS]] |
| - | [[Category: McGregor, N G.S]] | + | [[Category: Nin-Hill A]] |
| - | [[Category: Nin-Hill, A]] | + | [[Category: Rovira C]] |
| - | [[Category: Rovira, C]] | + | |
| - | [[Category: Arabinofuranosidase]]
| + | |
| - | [[Category: Aspergillus]]
| + | |
| - | [[Category: Covalent complex]]
| + | |
| - | [[Category: Gh54]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
6sxt is a 1 chain structure with sequence from Aspergillus luchuensis IFO 4308. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.466Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[1] [2]
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S. Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem. 2004 Oct 22;279(43):44907-14. Epub 2004 Aug 3. PMID:15292273 doi:10.1074/jbc.M405390200
- ↑ Koseki T, Okuda M, Sudoh S, Kizaki Y, Iwano K, Aramaki I, Matsuzawa H. Role of two alpha-L-arabinofuranosidases in arabinoxylan degradation and characteristics of the encoding genes from shochu koji molds, Aspergillus kawachii and Aspergillus awamori. J Biosci Bioeng. 2003;96(3):232-41. doi: 10.1016/s1389-1723(03)80187-1. PMID:16233515 doi:http://dx.doi.org/10.1016/s1389-1723(03)80187-1
- ↑ 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. Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-L-Arabinofuranosidases. J Am Chem Soc. 2020 Feb 13. doi: 10.1021/jacs.9b11351. PMID:32053363 doi:http://dx.doi.org/10.1021/jacs.9b11351
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