6t75 - Revision history

OCA at 12:56, 24 January 2024

2024-01-24T12:56:09Z

←Older revision		Revision as of 12:56, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6t75' size='340' side='right'caption='[[6t75]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='6t75' size='340' side='right'caption='[[6t75]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6t75]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_baa-997 Atcc baa-997~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T75 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6T75 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t75]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_salyersiae Bacteroides salyersiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T75 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=MAF:~~2~~-DEOXY-2-FLUORO-ALPHA-D-MANNOSE'>MAF</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]] 2.55Å</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=291644 ATCC BAA~~-~~997])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAF:2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE'>MAF</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6t75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t75 OCA], [~~http~~://pdbe.org/6t75 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6t75 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6t75 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6t75 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=6t75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t75 OCA], [https://pdbe.org/6t75 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t75 RCSB], [https://www.ebi.ac.uk/pdbsum/6t75 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t75 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I9SUA3_9BACE I9SUA3_9BACE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc baa-997~~]]	+	[[Category: Bacteroides salyersiae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Armstrong, Z]]	+	[[Category: Armstrong Z]]
-	[[Category: Davies, G]]	+	[[Category: Davies G]]
-	~~[[Category: Beta-mannosidase glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:24, 8 April 2020

2020-04-08T07:24:38Z

←Older revision		Revision as of 07:24, 8 April 2020
Line 3:		Line 3:
	<StructureSection load='6t75' size='340' side='right'caption='[[6t75]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='6t75' size='340' side='right'caption='[[6t75]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6t75]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_baa-997 Atcc baa-997]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T75 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6T75 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t75]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_baa-997 Atcc baa-997]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T75 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T75 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=MAF:2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE'>MAF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAF:2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE'>MAF</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=291644 ATCC BAA-997])</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=291644 ATCC BAA-997])</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=6t75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t75 OCA], [http://pdbe.org/6t75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t75 RCSB], [http://www.ebi.ac.uk/pdbsum/6t75 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t75 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6t75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t75 OCA], [http://pdbe.org/6t75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t75 RCSB], [http://www.ebi.ac.uk/pdbsum/6t75 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t75 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:45, 8 January 2020

2020-01-08T09:45:30Z

←Older revision		Revision as of 09:45, 8 January 2020
Line 3:		Line 3:
	<StructureSection load='6t75' size='340' side='right'caption='[[6t75]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='6t75' size='340' side='right'caption='[[6t75]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6t75]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T75 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T75 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t75]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_baa-997 Atcc baa-997]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T75 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T75 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=MAF:2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE'>MAF</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=MAF:2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE'>MAF</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=291644 ATCC BAA-997])</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=6t75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t75 OCA], [http://pdbe.org/6t75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t75 RCSB], [http://www.ebi.ac.uk/pdbsum/6t75 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t75 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=6t75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t75 OCA], [http://pdbe.org/6t75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t75 RCSB], [http://www.ebi.ac.uk/pdbsum/6t75 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t75 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 6t75" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc baa-997]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]

OCA at 08:25, 1 January 2020

2020-01-01T08:25:31Z

←Older revision		Revision as of 08:25, 1 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6t75 is ON HOLD~~	+	==Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzyme intermediate==
-		+	<StructureSection load='6t75' size='340' side='right'caption='[[6t75]], [[Resolution\|resolution]] 2.55Å' scene=''>
-	~~Authors: Armstrong, Z., Davies, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6t75]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T75 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T75 FirstGlance]. <br>
-	~~Description:~~ Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzyme intermediate	+	</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=MAF:2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE'>MAF</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6t75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t75 OCA], [http://pdbe.org/6t75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t75 RCSB], [http://www.ebi.ac.uk/pdbsum/6t75 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t75 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]
	[[Category: Davies, G]]		[[Category: Davies, G]]
		+	[[Category: Beta-mannosidase glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA: Protected "6t75" [edit=sysop:move=sysop]

2019-10-30T07:28:51Z

Protected "6t75" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:28, 30 October 2019

OCA: New page: '''Unreleased structure''' The entry 6t75 is ON HOLD Authors: Armstrong, Z., Davies, G. Description: Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzy...

2019-10-30T07:28:50Z

New page: '''Unreleased structure''' The entry 6t75 is ON HOLD Authors: Armstrong, Z., Davies, G. Description: Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzy...

New page

'''Unreleased structure'''

The entry 6t75 is ON HOLD

Authors: Armstrong, Z., Davies, G.

Description: Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzyme intermediate
[[Category: Unreleased Structures]]
[[Category: Armstrong, Z]]
[[Category: Davies, G]]