5glp: Difference between revisions
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==Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose, calcium-bound form== | ==Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose, calcium-bound form== | ||
<StructureSection load='5glp' size='340' side='right' caption='[[5glp]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='5glp' size='340' side='right'caption='[[5glp]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5glp]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5glp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GLP 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=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5glp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glp OCA], [https://pdbe.org/5glp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5glp RCSB], [https://www.ebi.ac.uk/pdbsum/5glp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5glp ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0H5BL38_9BACT A0A0H5BL38_9BACT] | |||
<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: | [[Category: Large Structures]] | ||
[[Category: Fujimoto | [[Category: Uncultured bacterium]] | ||
[[Category: Kishine | [[Category: Fujimoto Z]] | ||
[[Category: Matsuzawa | [[Category: Kishine N]] | ||
[[Category: Yaoi | [[Category: Matsuzawa T]] | ||
[[Category: Yaoi K]] | |||
Latest revision as of 14:35, 2 August 2023
Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose, calcium-bound formCrystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose, calcium-bound form
Structural highlights
FunctionPublication Abstract from PubMedThe crystal structure of metagenomic beta-xylosidase/alpha-l-arabinofuranosidase CoXyl43, activated by calcium ions, was determined in its apo and complexed forms with xylotriose or l-arabinose in the presence and absence of calcium. The presence of calcium ions dramatically increases the kcat of CoXyl43 for p-nitrophenyl beta-d-xylopyranoside and reduces the Michaelis constant for p-nitrophenyl alpha-l-arabinofuranoside. CoXyl43 consists of a single catalytic domain comprised of a five-bladed beta-propeller. In the presence of calcium, a single calcium ion was observed at the centre of this catalytic domain, behind the catalytic pocket. In the absence of calcium, the calcium ion was replaced with one sodium ion and one water molecule, and the positions of these cations were shifted by 1.3 A. The histidine-319 side chain, which coordinates to the 2-hydroxyl oxygen atom of the bound xylose molecule in the catalytic pocket, also coordinates to the calcium ion, but not to the sodium ion. The calcium-dependent increase in activity appears to be caused by the structural change in the catalytic pocket induced by the tightly bound calcium ion and coordinating water molecules, and by the protonation state of glutamic acid-268, the catalytic acid of the enzyme. Our findings further elucidate the complex relationship between metal ions and glycosidases. Crystal structure of metagenomic beta-xylosidase/ alpha-l-arabinofuranosidase activated by calcium.,Matsuzawa T, Kaneko S, Kishine N, Fujimoto Z, Yaoi K J Biochem. 2017 Sep 1;162(3):173-181. doi: 10.1093/jb/mvx012. PMID:28204531[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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