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6sxs

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Revision as of 10:28, 18 March 2020

GH54 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor

Structural highlights

6sxs is a 1 chain structure with sequence from Aspka. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , ,
Gene:	abfB, AKAW_08685 (ASPKA)
Activity:	Non-reducing end alpha-L-arabinofuranosidase, with EC number 3.2.1.55
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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6sxs"

@@ Line 3: / Line 3: @@
 <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. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SXS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6sxs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspka Aspka]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SXS 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=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='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=40384 ASPKA])</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=6sxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sxs OCA], [http://pdbe.org/6sxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sxs RCSB], [http://www.ebi.ac.uk/pdbsum/6sxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sxs ProSAT]</span></td></tr>
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Aspka]]
 [[Category: Large Structures]]
 [[Category: Non-reducing end alpha-L-arabinofuranosidase]]

6sxs

From Proteopedia

Revision as of 10:28, 18 March 2020

GH54 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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