3c7o: Difference between revisions

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<StructureSection load='3c7o' size='340' side='right'caption='[[3c7o]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3c7o' size='340' side='right'caption='[[3c7o]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3c7o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C7O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C7O FirstGlance]. <br>
<table><tr><td colspan='2'>[[3c7o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C7O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C7O FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3c7e|3c7e]], [[3c7f|3c7f]], [[3c7g|3c7g]], [[3c7h|3c7h]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900011:beta-cellotetraose'>PRD_900011</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xynD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [https://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=3c7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c7o OCA], [https://pdbe.org/3c7o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c7o RCSB], [https://www.ebi.ac.uk/pdbsum/3c7o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c7o ProSAT]</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=3c7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c7o OCA], [https://pdbe.org/3c7o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c7o RCSB], [https://www.ebi.ac.uk/pdbsum/3c7o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c7o ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/XYND_BACSU XYND_BACSU]] Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation. Is more active on wheat bran AXOS than on wheat water-extractable AX and rye water-extractable AX. Does not display endoxylanase, xylosidase or arabinanase activity.<ref>PMID:17426966</ref>
[https://www.uniprot.org/uniprot/XYND_BACSU XYND_BACSU] Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation. Is more active on wheat bran AXOS than on wheat water-extractable AX and rye water-extractable AX. Does not display endoxylanase, xylosidase or arabinanase activity.<ref>PMID:17426966</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c7o ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c7o ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
AXHs (arabinoxylan arabinofuranohydrolases) are alpha-L-arabinofuranosidases that specifically hydrolyse the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. Bacillus subtilis was recently shown to produce an AXH that cleaves arabinose units from O-2- or O-3-mono-substituted xylose residues: BsAXH-m2,3 (B. subtilis AXH-m2,3). Crystallographic analysis reveals a two-domain structure for this enzyme: a catalytic domain displaying a five-bladed beta-propeller fold characteristic of GH (glycoside hydrolase) family 43 and a CBM (carbohydrate-binding module) with a beta-sandwich fold belonging to CBM family 6. Binding of substrate to BsAXH-m2,3 is largely based on hydrophobic stacking interactions, which probably allow the positional flexibility needed to hydrolyse both arabinose substituents at the O-2 or O-3 position of the xylose unit. Superposition of the BsAXH-m2,3 structure with known structures of the GH family 43 exo-acting enzymes, beta-xylosidase and alpha-L-arabinanase, each in complex with their substrate, reveals a different orientation of the sugar backbone.
Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family.,Vandermarliere E, Bourgois TM, Winn MD, van Campenhout S, Volckaert G, Delcour JA, Strelkov SV, Rabijns A, Courtin CM Biochem J. 2009 Feb 15;418(1):39-47. PMID:18980579<ref>PMID:18980579</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3c7o" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Non-reducing end alpha-L-arabinofuranosidase]]
[[Category: Bourgois TM]]
[[Category: Bourgois, T M]]
[[Category: Courtin CM]]
[[Category: Campenhout, S Van]]
[[Category: Delcour JA]]
[[Category: Courtin, C M]]
[[Category: Rabijns A]]
[[Category: Delcour, J A]]
[[Category: Strelkov SV]]
[[Category: Rabijns, A]]
[[Category: Van Campenhout S]]
[[Category: Strelkov, S V]]
[[Category: Vandermarliere E]]
[[Category: Vandermarliere, E]]
[[Category: Volckaert G]]
[[Category: Volckaert, G]]
[[Category: Winn MD]]
[[Category: Winn, M D]]
[[Category: 5-bladed beta-propeller fold]]
[[Category: Beta-sandwich]]
[[Category: Hydrolase]]
[[Category: Xylan degradation]]
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