5fq3 - Revision history

OCA at 07:22, 1 May 2024

OCA — Wed, 01 May 2024 07:22:58 GMT

←Older revision		Revision as of 07:22, 1 May 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q8A5H7_BACTN Q8A5H7_BACTN]		[https://www.uniprot.org/uniprot/Q8A5H7_BACTN Q8A5H7_BACTN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The human large intestine is populated by a high density of microorganisms, collectively termed the colonic microbiota, which has an important role in human health and nutrition. The survival of microbiota members from the dominant Gram-negative phylum Bacteroidetes depends on their ability to degrade dietary glycans that cannot be metabolized by the host. The genes encoding proteins involved in the degradation of specific glycans are organized into co-regulated polysaccharide utilization loci, with the archetypal locus sus (for starch utilisation system) encoding seven proteins, SusA-SusG. Glycan degradation mainly occurs intracellularly and depends on the import of oligosaccharides by an outer membrane protein complex composed of an extracellular SusD-like lipoprotein and an integral membrane SusC-like TonB-dependent transporter. The presence of the partner SusD-like lipoprotein is the major feature that distinguishes SusC-like proteins from previously characterized TonB-dependent transporters. Many sequenced gut Bacteroides spp. encode over 100 SusCD pairs, of which the majority have unknown functions and substrate specificities. The mechanism by which extracellular substrate binding by SusD proteins is coupled to outer membrane passage through their cognate SusC transporter is unknown. Here we present X-ray crystal structures of two functionally distinct SusCD complexes purified from Bacteroides thetaiotaomicron and derive a general model for substrate translocation. The SusC transporters form homodimers, with each beta-barrel protomer tightly capped by SusD. Ligands are bound at the SusC-SusD interface in a large solvent-excluded cavity. Molecular dynamics simulations and single-channel electrophysiology reveal a 'pedal bin' mechanism, in which SusD moves away from SusC in a hinge-like fashion in the absence of ligand to expose the substrate-binding site to the extracellular milieu. These data provide mechanistic insights into outer membrane nutrient import by members of the microbiota, an area of major importance for understanding human-microbiota symbiosis.
-
-	Structural basis for nutrient acquisition by dominant members of the human gut microbiota.,Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Basle A, Firbank SJ, Zheng H, Robinson CV, Winterhalter M, Kleinekathofer U, Bolam DN, van den Berg B Nature. 2017 Jan 19;541(7637):407-411. doi: 10.1038/nature20828. Epub 2017 Jan, 11. PMID:28077872<ref>PMID:28077872</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5fq3" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:18, 26 July 2023

OCA — Wed, 26 Jul 2023 13:18:11 GMT

←Older revision		Revision as of 13:18, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='5fq3' size='340' side='right'caption='[[5fq3]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='5fq3' size='340' side='right'caption='[[5fq3]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fq3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_thetaiotaomicron"_distaso_1912 "bacillus~~ thetaiotaomicron~~" distaso 1912~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FQ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fq3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FQ3 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fq4\|5fq4]]~~, [[~~5fq6~~\|~~5fq6]], [[5fq7\|5fq7]], [[5fq8\|5fq8~~]]</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]] 3.1Å</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=5fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq3 OCA], [~~http~~://pdbe.org/5fq3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fq3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fq3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq3 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=5fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq3 OCA], [https://pdbe.org/5fq3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fq3 RCSB], [https://www.ebi.ac.uk/pdbsum/5fq3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8A5H7_BACTN Q8A5H7_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ thetaiotaomicron ~~distaso 1912~~]]	+	[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basle, A]]	+	[[Category: Basle A]]
-	~~[[Category: Berg, B van den~~]]	+	[[Category: Bolam DN]]
-	[[Category: Bolam~~, D N~~]]	+	[[Category: Chorev DS]]
-	[[Category: Chorev~~, D S~~]]	+	[[Category: Glenwright AJ]]
-	[[Category: Glenwright~~, A J~~]]	+	[[Category: Kleinekathoefer U]]
-	[[Category: Kleinekathoefer, U]]	+	[[Category: Pothula KR]]
-	[[Category: Pothula~~, K R~~]]	+	[[Category: Robinson CV]]
-	[[Category: Robinson~~, C V~~]]	+	[[Category: Van den Berg B]]
-	[[Category: ~~Membrane protein]]~~	+
-	~~[[Category: Outer membrane lipoprotein~~]]	+

OCA at 07:31, 6 May 2020

OCA — Wed, 06 May 2020 07:31:42 GMT

←Older revision		Revision as of 07:31, 6 May 2020
Line 1:		Line 1:

	==Crystal structure of the lipoprotein BT2262 from Bacteroides thetaiotaomicron==		==Crystal structure of the lipoprotein BT2262 from Bacteroides thetaiotaomicron==
-	<StructureSection load='5fq3' size='340' side='right' caption='[[5fq3]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='5fq3' size='340' side='right'caption='[[5fq3]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fq3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FQ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fq3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FQ3 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fq4\|5fq4]], [[5fq6\|5fq6]], [[5fq7\|5fq7]], [[5fq8\|5fq8]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fq4\|5fq4]], [[5fq6\|5fq6]], [[5fq7\|5fq7]], [[5fq8\|5fq8]]</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=5fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq3 OCA], [http://pdbe.org/5fq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq3 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=5fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq3 OCA], [http://pdbe.org/5fq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus thetaiotaomicron distaso 1912]]
		+	[[Category: Large Structures]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Berg, B van den]]		[[Category: Berg, B van den]]

OCA at 16:24, 25 January 2017

OCA — Wed, 25 Jan 2017 16:24:32 GMT

←Older revision		Revision as of 16:24, 25 January 2017
Line 7:		Line 7:
	<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=5fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq3 OCA], [http://pdbe.org/5fq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq3 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=5fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq3 OCA], [http://pdbe.org/5fq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq3 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human large intestine is populated by a high density of microorganisms, collectively termed the colonic microbiota, which has an important role in human health and nutrition. The survival of microbiota members from the dominant Gram-negative phylum Bacteroidetes depends on their ability to degrade dietary glycans that cannot be metabolized by the host. The genes encoding proteins involved in the degradation of specific glycans are organized into co-regulated polysaccharide utilization loci, with the archetypal locus sus (for starch utilisation system) encoding seven proteins, SusA-SusG. Glycan degradation mainly occurs intracellularly and depends on the import of oligosaccharides by an outer membrane protein complex composed of an extracellular SusD-like lipoprotein and an integral membrane SusC-like TonB-dependent transporter. The presence of the partner SusD-like lipoprotein is the major feature that distinguishes SusC-like proteins from previously characterized TonB-dependent transporters. Many sequenced gut Bacteroides spp. encode over 100 SusCD pairs, of which the majority have unknown functions and substrate specificities. The mechanism by which extracellular substrate binding by SusD proteins is coupled to outer membrane passage through their cognate SusC transporter is unknown. Here we present X-ray crystal structures of two functionally distinct SusCD complexes purified from Bacteroides thetaiotaomicron and derive a general model for substrate translocation. The SusC transporters form homodimers, with each beta-barrel protomer tightly capped by SusD. Ligands are bound at the SusC-SusD interface in a large solvent-excluded cavity. Molecular dynamics simulations and single-channel electrophysiology reveal a 'pedal bin' mechanism, in which SusD moves away from SusC in a hinge-like fashion in the absence of ligand to expose the substrate-binding site to the extracellular milieu. These data provide mechanistic insights into outer membrane nutrient import by members of the microbiota, an area of major importance for understanding human-microbiota symbiosis.
		+
		+	Structural basis for nutrient acquisition by dominant members of the human gut microbiota.,Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Basle A, Firbank SJ, Zheng H, Robinson CV, Winterhalter M, Kleinekathofer U, Bolam DN, van den Berg B Nature. 2017 Jan 19;541(7637):407-411. doi: 10.1038/nature20828. Epub 2017 Jan, 11. PMID:28077872<ref>PMID:28077872</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fq3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:15, 15 December 2016

OCA — Thu, 15 Dec 2016 19:15:03 GMT

←Older revision		Revision as of 19:15, 15 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5fq3 is ON HOLD until Paper Publication~~	+	==Crystal structure of the lipoprotein BT2262 from Bacteroides thetaiotaomicron==
-		+	<StructureSection load='5fq3' size='340' side='right' caption='[[5fq3]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~Authors: Glenwright, A.J., Pothula, K.R., Chorev, D.S., Basle, A., Robinson, C.V., Kleinekathoefer, U., Bolam, D.N., van den Berg, B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fq3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FQ3 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the lipoprotein BT2262 from Bacteroides thetaiotaomicron	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fq4\|5fq4]], [[5fq6\|5fq6]], [[5fq7\|5fq7]], [[5fq8\|5fq8]]</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=5fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq3 OCA], [http://pdbe.org/5fq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq3 ProSAT]</span></td></tr>
-	[[~~Category: Glenwright, A.J~~]]	+	</table>
-	[[~~Category~~: ~~Bolam, D~~.N]]	+	__TOC__
-	[[~~Category~~: ~~Pothula~~, ~~K.R~~]]	+	</StructureSection>
-	[[~~Category: Van Den Berg~~, B]]	+
-	[[~~Category~~: ~~Chorev~~, D.S]]	+
-	[~~[Category~~: ~~Robinson~~, C.V]]	+
	[[Category: Basle, A]]		[[Category: Basle, A]]
		+	[[Category: Berg, B van den]]
		+	[[Category: Bolam, D N]]
		+	[[Category: Chorev, D S]]
		+	[[Category: Glenwright, A J]]
	[[Category: Kleinekathoefer, U]]		[[Category: Kleinekathoefer, U]]
		+	[[Category: Pothula, K R]]
		+	[[Category: Robinson, C V]]
		+	[[Category: Membrane protein]]
		+	[[Category: Outer membrane lipoprotein]]

OCA at 18:31, 13 January 2016

OCA — Wed, 13 Jan 2016 18:31:32 GMT

←Older revision		Revision as of 18:31, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fq3 is ON HOLD	+	The entry 5fq3 is ON HOLD until Paper Publication

	Authors: Glenwright, A.J., Pothula, K.R., Chorev, D.S., Basle, A., Robinson, C.V., Kleinekathoefer, U., Bolam, D.N., van den Berg, B.		Authors: Glenwright, A.J., Pothula, K.R., Chorev, D.S., Basle, A., Robinson, C.V., Kleinekathoefer, U., Bolam, D.N., van den Berg, B.

OCA: Protected "5fq3" [edit=sysop:move=sysop]

OCA — Wed, 16 Dec 2015 13:01:11 GMT

Protected "5fq3" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:01, 16 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fq3 is ON HOLD Authors: Glenwright, A.J., Pothula, K.R., Chorev, D.S., Basle, A., Robinson, C.V., Kleinekathoefer, U., Bolam, D.N., van den Berg, B...

OCA — Wed, 16 Dec 2015 13:01:09 GMT

New page: '''Unreleased structure''' The entry 5fq3 is ON HOLD Authors: Glenwright, A.J., Pothula, K.R., Chorev, D.S., Basle, A., Robinson, C.V., Kleinekathoefer, U., Bolam, D.N., van den Berg, B...

New page

'''Unreleased structure'''

The entry 5fq3 is ON HOLD

Authors: Glenwright, A.J., Pothula, K.R., Chorev, D.S., Basle, A., Robinson, C.V., Kleinekathoefer, U., Bolam, D.N., van den Berg, B.

Description: Crystal structure of the lipoprotein BT2262 from Bacteroides thetaiotaomicron
[[Category: Unreleased Structures]]
[[Category: Glenwright, A.J]]
[[Category: Bolam, D.N]]
[[Category: Pothula, K.R]]
[[Category: Van Den Berg, B]]
[[Category: Chorev, D.S]]
[[Category: Robinson, C.V]]
[[Category: Basle, A]]
[[Category: Kleinekathoefer, U]]