6t7g: Difference between revisions
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<StructureSection load='6t7g' size='340' side='right'caption='[[6t7g]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='6t7g' size='340' side='right'caption='[[6t7g]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6t7g]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T7G FirstGlance]. <br> | <table><tr><td colspan='2'>[[6t7g]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_salyersae_cl02t12c01 Bacteroides salyersae cl02t12c01]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T7G FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MVL:(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>MVL</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HMPREF1071_03408 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=997887 Bacteroides salyersae CL02T12C01])</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=6t7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t7g OCA], [http://pdbe.org/6t7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t7g RCSB], [http://www.ebi.ac.uk/pdbsum/6t7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t7g 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=6t7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t7g OCA], [http://pdbe.org/6t7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t7g RCSB], [http://www.ebi.ac.uk/pdbsum/6t7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t7g ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Recent work exploring protein sequence space has revealed a new glycoside hydrolase (GH) family (GH164) of putative mannosidases. GH164 genes are present in several commensal bacteria, implicating these genes in the degradation of dietary glycans. However, little is known about the structure, mechanism of action and substrate specificity of these enzymes. Herein we report the biochemical characterization and crystal structures of the founding member of this family (Bs164) from the human gut symbiont Bacteroides salyersiae. Previous reports of this enzyme indicated that it has alpha-mannosidase activity, however we conclusively show that it cleaves only beta-mannose linkages. Using NMR spectroscopy, detailed enzyme kinetics of wild-type and mutant Bs164, and multi-angle light scattering we found that it is a trimeric retaining beta-mannosidase, that is susceptible to several known mannosidase inhibitors. X-ray crystallography revealed the structure of Bs164 - the first known structure of a GH164 - at 1.91 A resolution. Bs164 is composed of three domains: a (beta/alpha)8 barrel, a trimerization domain and a beta-sandwich domain, representing a previously unobserved structural fold for beta-mannosidases. Structures of Bs164 at 1.80-2.55 A resolution in complex with the inhibitors noeuromycin, mannoimidazole or DNP 2-deoxy-2-fluoro-mannose reveal the residues essential for specificity and catalysis including the catalytic nucleophile (Glu297) and acid/base residue (Glu160). These findings further our knowledge of the mechanisms commensal microbes use for nutrient acquisition. | |||
Structure and function of Bs164 beta-mannosidase from Bacteroides salyersiae the founding member of glycoside hydrolase family GH164.,Armstrong Z, Davies GJ J Biol Chem. 2019 Dec 22. pii: RA119.011591. doi: 10.1074/jbc.RA119.011591. PMID:31871050<ref>PMID:31871050</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6t7g" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacteroides salyersae cl02t12c01]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Armstrong, Z]] | [[Category: Armstrong, Z]] | ||