View source for 8qf2


==Beta-L-Arabinofurano-cyclitol Aziridines are Cysteine-directed Broad-spectrum Inhibitors and Activity-based Probes for Retaining Beta-L-arabinofuranosidases==
<StructureSection load='8qf2' size='340' side='right'caption='[[8qf2]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8qf2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8QF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QF2 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]] 2.35&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UI5:(1~{S},2~{S},3~{S},4~{R})-4-azanyl-3-(hydroxymethyl)cyclopentane-1,2-diol'>UI5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8qf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qf2 OCA], [https://pdbe.org/8qf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qf2 RCSB], [https://www.ebi.ac.uk/pdbsum/8qf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qf2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HYBA1_BIFL2 HYBA1_BIFL2] Beta-L-arabinofuranosidase that removes the beta-L-arabinofuranose residue from the non-reducing end of various substrates, including beta-L-arabinofuranosyl-hydroxyproline (Ara-Hyp), Ara-beta-1,2-Ara-beta-Hyp (Ara(2)-Hyp), Ara-beta-1,2-Ara-beta-1,2-Ara-beta-Hyp (Ara(3)-Hyp), and beta-L-arabinofuranosyl-(1->2)-1-O-methyl-beta-L-arabinofuranose. In the presence of 1-alkanols, shows transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.
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== Publication Abstract from PubMed ==
GH127 and GH146 microorganismal retaining beta-l-arabinofuranosidases, expressed by human gut microbiomes, feature an atypical catalytic domain and an unusual mechanism of action. We recently reported that both Bacteroides thetaiotaomicron BtGH146 and Bifidobacterium longum HypBA1 are inhibited by beta-l-arabinofuranosyl cyclophellitol epoxide, supporting the action of a zinc-coordinated cysteine as a catalytic nucleophile, where in most retaining GH families, an aspartate or glutamate is employed. This work presents a panel of beta-l-arabinofuranosyl cyclophellitol epoxides and aziridines as mechanism-based BtGH146/HypBA1 inhibitors and activity-based probes. The beta-l-arabinofuranosyl cyclophellitol aziridines both inhibit and label beta-l-arabinofuranosidase efficiently (however with different activities), whereas the epoxide-derived probes favor BtGH146 over HypBA1. These findings are accompanied by X-ray structural analysis of the unmodified beta-l-arabinofuranosyl cyclophellitol aziridine in complex with both isozymes, which were shown to react by nucleophilic opening of the aziridine, at the pseudoanomeric carbon, by the active site cysteine nucleophile to form a stable thioether bond. Altogether, our activity-based probes may serve as chemical tools for the detection and identification of low-abundance beta-l-arabinofuranosidases in complex biological samples.

beta-l-Arabinofurano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining beta-l-Arabinofuranosidases.,Borlandelli V, Offen W, Moroz O, Nin-Hill A, McGregor N, Binkhorst L, Ishiwata A, Armstrong Z, Artola M, Rovira C, Davies GJ, Overkleeft HS ACS Chem Biol. 2023 Dec 15;18(12):2564-2573. doi: 10.1021/acschembio.3c00558. , Epub 2023 Dec 5. PMID:38051515<ref>PMID:38051515</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 8qf2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bifidobacterium longum]]
[[Category: Large Structures]]
[[Category: Armstrong Z]]
[[Category: Artola M]]
[[Category: Binkhorst L]]
[[Category: Borlandelli V]]
[[Category: Davies GJ]]
[[Category: Ishiwata A]]
[[Category: McGregor N]]
[[Category: Moroz O]]
[[Category: Nin-Hill A]]
[[Category: Offen WA]]
[[Category: Overkleeft H]]
[[Category: Rovira C]]