6mpa - Revision history

OCA at 14:44, 13 March 2024

OCA — Wed, 13 Mar 2024 14:44:23 GMT

←Older revision		Revision as of 14:44, 13 March 2024
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	<StructureSection load='6mpa' size='340' side='right'caption='[[6mpa]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6mpa' size='340' side='right'caption='[[6mpa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mpa]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bifld Bifld~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MPA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mpa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_DJO10A Bifidobacterium longum DJO10A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MPA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FLC:CITRATE+ANION'>FLC</scene~~>, ~~<scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~BLD_0195 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=205913 BIFLD])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=6mpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mpa OCA], [~~http~~://pdbe.org/6mpa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mpa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mpa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mpa 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=6mpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mpa OCA], [https://pdbe.org/6mpa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mpa RCSB], [https://www.ebi.ac.uk/pdbsum/6mpa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mpa ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/B3DQP5_BIFLD B3DQP5_BIFLD]
-	Bifidobacteria represent one of the first colonizers of human gut microbiota, providing to this ecosystem better health and nutrition. To maintain a mutualistic relationship, they have enzymes to degrade and use complex carbohydrates non-digestible by their hosts. To succeed in the densely populated gut environment, they evolved molecular strategies that remain poorly understood. Herein, we report a novel mechanism found in probiotic Bifidobacteria for the depolymerization of the ubiquitous 2-acetamido-2-deoxy-4-O-(beta-d-mannopyranosyl)-d-glucopyranose (Man-beta-1,4-GlcNAc), a disaccharide that composes the universal core of eukaryotic N-glycans. In contrast to Bacteroidetes, these Bifidobacteria have a specialist and strain-specific beta-mannosidase that contains three distinctive structural elements conferring high selectivity for Man-beta-1,4-GlcNAc: a lid that undergoes conformational changes upon substrate binding, a tryptophan residue swapped between the two dimeric subunits to accommodate the GlcNAc moiety, and a Rossmann fold subdomain strategically located near to the active site pocket. These key structural elements for Man-beta-1,4-GlcNAc specificity are highly conserved in Bifidobacterium species adapted to the gut of a wide range of social animals, including bee, pig, rabbit, and human. ~~Together, our findings uncover an unprecedented molecular strategy employed by Bifidobacteria to selectively uptake carbohydrates from N-glycans in social hosts~~.	+

-	N-glycan Utilization by Bifidobacterium Gut Symbionts Involves a Specialist beta-Mannosidase.,Cordeiro RL, Pirolla RAS, Persinoti GF, Gozzo FC, de Giuseppe PO, Murakami MT J Mol Biol. 2019 Jan 11. pii: S0022-2836(19)30006-3. doi:, 10.1016/j.jmb.2018.12.017. PMID:30641082<ref>PMID:30641082</ref>	+	==See Also==
-		+	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6mpa" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bifld~~]]	+	[[Category: Bifidobacterium longum DJO10A]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Giuseppe~~, P O~~]]	+	[[Category: Giuseppe PO]]
-	[[Category: Lorizolla-Cordeiro, R]]	+	[[Category: Lorizolla-Cordeiro R]]
-	[[Category: Murakami~~, M T]]~~	+	[[Category: Murakami MT]]
-	~~[[Category: Beta-mannosidase]]~~	+
-	~~[[Category: Family gh5]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Subfamily 18~~]]	+

OCA at 11:26, 1 January 2020

OCA — Wed, 01 Jan 2020 11:26:32 GMT

←Older revision		Revision as of 11:26, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of BlMan5B in complex with GlcNAc (soaking)==		==Crystal structure of BlMan5B in complex with GlcNAc (soaking)==
-	<StructureSection load='6mpa' size='340' side='right' caption='[[6mpa]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6mpa' size='340' side='right'caption='[[6mpa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6mpa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifld Bifld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MPA FirstGlance]. <br>		<table><tr><td colspan='2'>[[6mpa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifld Bifld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MPA FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bifld]]		[[Category: Bifld]]
		+	[[Category: Large Structures]]
	[[Category: Giuseppe, P O]]		[[Category: Giuseppe, P O]]
	[[Category: Lorizolla-Cordeiro, R]]		[[Category: Lorizolla-Cordeiro, R]]

OCA at 16:06, 27 February 2019

OCA — Wed, 27 Feb 2019 16:06:29 GMT

←Older revision		Revision as of 16:06, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='6mpa' size='340' side='right' caption='[[6mpa]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6mpa' size='340' side='right' caption='[[6mpa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mpa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mpa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifld Bifld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MPA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BLD_0195 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=205913 BIFLD])</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=6mpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mpa OCA], [http://pdbe.org/6mpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mpa RCSB], [http://www.ebi.ac.uk/pdbsum/6mpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mpa 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=6mpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mpa OCA], [http://pdbe.org/6mpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mpa RCSB], [http://www.ebi.ac.uk/pdbsum/6mpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mpa ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bifld]]
	[[Category: Giuseppe, P O]]		[[Category: Giuseppe, P O]]
	[[Category: Lorizolla-Cordeiro, R]]		[[Category: Lorizolla-Cordeiro, R]]

OCA at 08:43, 30 January 2019

OCA — Wed, 30 Jan 2019 08:43:35 GMT

←Older revision		Revision as of 08:43, 30 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mpa is ~~ON HOLD~~	+	==Crystal structure of BlMan5B in complex with GlcNAc (soaking)==
		+	<StructureSection load='6mpa' size='340' side='right' caption='[[6mpa]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6mpa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MPA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=6mpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mpa OCA], [http://pdbe.org/6mpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mpa RCSB], [http://www.ebi.ac.uk/pdbsum/6mpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mpa ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bifidobacteria represent one of the first colonizers of human gut microbiota, providing to this ecosystem better health and nutrition. To maintain a mutualistic relationship, they have enzymes to degrade and use complex carbohydrates non-digestible by their hosts. To succeed in the densely populated gut environment, they evolved molecular strategies that remain poorly understood. Herein, we report a novel mechanism found in probiotic Bifidobacteria for the depolymerization of the ubiquitous 2-acetamido-2-deoxy-4-O-(beta-d-mannopyranosyl)-d-glucopyranose (Man-beta-1,4-GlcNAc), a disaccharide that composes the universal core of eukaryotic N-glycans. In contrast to Bacteroidetes, these Bifidobacteria have a specialist and strain-specific beta-mannosidase that contains three distinctive structural elements conferring high selectivity for Man-beta-1,4-GlcNAc: a lid that undergoes conformational changes upon substrate binding, a tryptophan residue swapped between the two dimeric subunits to accommodate the GlcNAc moiety, and a Rossmann fold subdomain strategically located near to the active site pocket. These key structural elements for Man-beta-1,4-GlcNAc specificity are highly conserved in Bifidobacterium species adapted to the gut of a wide range of social animals, including bee, pig, rabbit, and human. Together, our findings uncover an unprecedented molecular strategy employed by Bifidobacteria to selectively uptake carbohydrates from N-glycans in social hosts.

-	~~Authors: Lorizolla~~-Cordeiro, R., Giuseppe, P.O., ~~Murakami, M~~.T.	+	N-glycan Utilization by Bifidobacterium Gut Symbionts Involves a Specialist beta-Mannosidase.,Cordeiro RL, Pirolla RAS, Persinoti GF, Gozzo FC, de Giuseppe PO, Murakami MT J Mol Biol. 2019 Jan 11. pii: S0022-2836(19)30006-3. doi:, 10.1016/j.jmb.2018.12.017. PMID:30641082<ref>PMID:30641082</ref>

-	~~Description: Crystal structure~~ of ~~BlMan5B in complex with GlcNAc (soaking)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Giuseppe, P.O]]	+	<div class="pdbe-citations 6mpa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Giuseppe, P O]]
	[[Category: Lorizolla-Cordeiro, R]]		[[Category: Lorizolla-Cordeiro, R]]
-	[[Category: Murakami, M.T]]	+	[[Category: Murakami, M T]]
		+	[[Category: Beta-mannosidase]]
		+	[[Category: Family gh5]]
		+	[[Category: Hydrolase]]
		+	[[Category: Subfamily 18]]

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

OCA — Wed, 17 Oct 2018 06:35:49 GMT

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

←Older revision

Revision as of 06:35, 17 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mpa is ON HOLD Authors: Lorizolla-Cordeiro, R., Giuseppe, P.O., Murakami, M.T. Description: Crystal structure of BlMan5B in complex with GlcNAc (s...

OCA — Wed, 17 Oct 2018 06:35:47 GMT

New page: '''Unreleased structure''' The entry 6mpa is ON HOLD Authors: Lorizolla-Cordeiro, R., Giuseppe, P.O., Murakami, M.T. Description: Crystal structure of BlMan5B in complex with GlcNAc (s...

New page

'''Unreleased structure'''

The entry 6mpa is ON HOLD

Authors: Lorizolla-Cordeiro, R., Giuseppe, P.O., Murakami, M.T.

Description: Crystal structure of BlMan5B in complex with GlcNAc (soaking)
[[Category: Unreleased Structures]]
[[Category: Giuseppe, P.O]]
[[Category: Lorizolla-Cordeiro, R]]
[[Category: Murakami, M.T]]