View source for 3wkx


==Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum arabinose complex form==
<StructureSection load='3wkx' size='340' side='right'caption='[[3wkx]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3wkx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._longum_JCM_1217 Bifidobacterium longum subsp. longum JCM 1217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WKX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WKX 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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</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=3wkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wkx OCA], [https://pdbe.org/3wkx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wkx RCSB], [https://www.ebi.ac.uk/pdbsum/3wkx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wkx 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.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Enzymes acting on beta-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of beta-l-arabinofuranosyl oligosaccharides in plant cells. Recently, a beta-l-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked beta-l-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and beta-l-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional beta-sandwich domains, with one beta-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn(2+) coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the beta-l-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.

Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum.,Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, Fushinobu S Biochem Biophys Res Commun. 2014 Apr 25;447(1):32-7. doi:, 10.1016/j.bbrc.2014.03.096. Epub 2014 Mar 27. PMID:24680821<ref>PMID:24680821</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3wkx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bifidobacterium longum subsp. longum JCM 1217]]
[[Category: Large Structures]]
[[Category: Arakawa T]]
[[Category: Fujita K]]
[[Category: Ito T]]
[[Category: Saikawa K]]
[[Category: Wakagi T]]