5glk: Difference between revisions
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<StructureSection load='5glk' size='340' side='right' caption='[[5glk]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='5glk' size='340' side='right' caption='[[5glk]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5glk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GLK FirstGlance]. <br> | <table><tr><td colspan='2'>[[5glk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GLK 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | </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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gll|5gll]], [[5glm|5glm]], [[5gln|5gln]], [[5glo|5glo]], [[5glp|5glp]], [[5glq|5glq]], [[5glr|5glr]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gll|5gll]], [[5glm|5glm]], [[5gln|5gln]], [[5glo|5glo]], [[5glp|5glp]], [[5glq|5glq]], [[5glr|5glr]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">coxyl43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=77133 uncultivated bacterium])</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=5glk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glk OCA], [http://pdbe.org/5glk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5glk RCSB], [http://www.ebi.ac.uk/pdbsum/5glk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5glk ProSAT]</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=5glk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5glk OCA], [http://pdbe.org/5glk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5glk RCSB], [http://www.ebi.ac.uk/pdbsum/5glk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5glk ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The 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<ref>PMID:28204531</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5glk" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Uncultivated bacterium]] | |||
[[Category: Fujimoto, Z]] | [[Category: Fujimoto, Z]] | ||
[[Category: Kishine, N]] | [[Category: Kishine, N]] | ||
Revision as of 10:32, 6 December 2017
Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome, calcium-free form.Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome, calcium-free form.
Structural highlights
Publication 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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