5kc0 - Revision history

OCA at 09:58, 27 September 2023

OCA — Wed, 27 Sep 2023 09:58:02 GMT

←Older revision		Revision as of 09:58, 27 September 2023
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	==Crystal structure of TmRibU, hexagonal crystal form==		==Crystal structure of TmRibU, hexagonal crystal form==
-	<StructureSection load='5kc0' size='340' side='right' caption='[[5kc0]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='5kc0' size='340' side='right'caption='[[5kc0]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kc0]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thema Thema~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KC0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kc0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KC0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=BNG:B~~-~~NONYLGLUCOSIDE'>BNG</scene>~~, ~~<scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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]] 3.2001Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ribU, TM_1455 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=243274 THEMA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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=5kc0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc0 OCA], [~~http~~://pdbe.org/5kc0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kc0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kc0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc0 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=5kc0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc0 OCA], [https://pdbe.org/5kc0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kc0 RCSB], [https://www.ebi.ac.uk/pdbsum/5kc0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RIBU_THEMA RIBU_THEMA]] Substrate-binding (S) component of an energy-coupling factor (ECF) ABC-transporter complex. Mediates riboflavin uptake, may also transport FMN and roseoflavin. Probably a riboflavin-binding protein that interacts with the energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins (Probable). Expression of the complex plus RibU in E.coli allows riboflavin uptake; uptake does not occur in the absence of RibU or the EcfA1A2T complex.<ref>PMID:23359690</ref>	+	[https://www.uniprot.org/uniprot/RIBU_THEMA RIBU_THEMA] Substrate-binding (S) component of an energy-coupling factor (ECF) ABC-transporter complex. Mediates riboflavin uptake, may also transport FMN and roseoflavin. Probably a riboflavin-binding protein that interacts with the energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins (Probable). Expression of the complex plus RibU in E.coli allows riboflavin uptake; uptake does not occur in the absence of RibU or the EcfA1A2T complex.<ref>PMID:23359690</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thema~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Karpowich, N K~~]]	+	[[Category: Thermotoga maritima MSB8]]
-	[[Category: ~~Song, J M~~]]	+	[[Category: Karpowich NK]]
-	[[Category: ~~Wang, D N~~]]	+	[[Category: Song JM]]
-	[[Category: ~~Integral membrane protein]]~~	+	[[Category: Wang DN]]
-	~~[[Category: Membrane transport]]~~	+
-	~~[[Category: Thermophile]]~~	+
-	~~[[Category: Transport protein-membrane protein complex]]~~	+
-	~~[[Category: Vitamin~~]]	+

OCA at 06:04, 1 November 2017

OCA — Wed, 01 Nov 2017 06:04:25 GMT

←Older revision		Revision as of 06:04, 1 November 2017
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	<StructureSection load='5kc0' size='340' side='right' caption='[[5kc0]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='5kc0' size='340' side='right' caption='[[5kc0]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kc0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KC0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kc0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KC0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribU, TM_1455 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=5kc0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc0 OCA], [http://pdbe.org/5kc0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kc0 RCSB], [http://www.ebi.ac.uk/pdbsum/5kc0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc0 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=5kc0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc0 OCA], [http://pdbe.org/5kc0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kc0 RCSB], [http://www.ebi.ac.uk/pdbsum/5kc0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc0 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Thema]]
	[[Category: Karpowich, N K]]		[[Category: Karpowich, N K]]
	[[Category: Song, J M]]		[[Category: Song, J M]]

OCA at 10:28, 13 July 2016

OCA — Wed, 13 Jul 2016 10:28:39 GMT

←Older revision		Revision as of 10:28, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kc0 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of TmRibU, hexagonal crystal form==
		+	<StructureSection load='5kc0' size='340' side='right' caption='[[5kc0]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kc0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KC0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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=5kc0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc0 OCA], [http://pdbe.org/5kc0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kc0 RCSB], [http://www.ebi.ac.uk/pdbsum/5kc0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc0 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIBU_THEMA RIBU_THEMA]] Substrate-binding (S) component of an energy-coupling factor (ECF) ABC-transporter complex. Mediates riboflavin uptake, may also transport FMN and roseoflavin. Probably a riboflavin-binding protein that interacts with the energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins (Probable). Expression of the complex plus RibU in E.coli allows riboflavin uptake; uptake does not occur in the absence of RibU or the EcfA1A2T complex.<ref>PMID:23359690</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein-substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface in which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.

-	~~Authors:~~ Karpowich, ~~N.K.~~, Wang~~, D~~.N., ~~Song, J~~.M.	+	An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin.,Karpowich NK, Song J, Wang DN J Mol Biol. 2016 Jun 13. pii: S0022-2836(16)30211-X. doi:, 10.1016/j.jmb.2016.06.003. PMID:27312125<ref>PMID:27312125</ref>

-	~~Description: Crystal structure of TmRibU~~, ~~hexagonal crystal form~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Song, J.M]]	+	<div class="pdbe-citations 5kc0" style="background-color:#fffaf0;"></div>
-	[[Category: Wang, D.N]]	+	== References ==
-	[[Category: ~~Karpowich, N.K~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Karpowich, N K]]
		+	[[Category: Song, J M]]
		+	[[Category: Wang, D N]]
		+	[[Category: Integral membrane protein]]
		+	[[Category: Membrane transport]]
		+	[[Category: Thermophile]]
		+	[[Category: Transport protein-membrane protein complex]]
		+	[[Category: Vitamin]]

OCA at 21:22, 23 June 2016

OCA — Thu, 23 Jun 2016 21:22:09 GMT

←Older revision		Revision as of 21:22, 23 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kc0 is ON HOLD	+	The entry 5kc0 is ON HOLD until Paper Publication

	Authors: Karpowich, N.K., Wang, D.N., Song, J.M.		Authors: Karpowich, N.K., Wang, D.N., Song, J.M.

OCA: Protected "5kc0" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 13:42:16 GMT

Protected "5kc0" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:42, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kc0 is ON HOLD Authors: Karpowich, N.K., Wang, D.N., Song, J.M. Description: Crystal structure of TmRibU, hexagonal crystal form [[Category: Unrel...

OCA — Mon, 20 Jun 2016 13:42:15 GMT

New page: '''Unreleased structure''' The entry 5kc0 is ON HOLD Authors: Karpowich, N.K., Wang, D.N., Song, J.M. Description: Crystal structure of TmRibU, hexagonal crystal form [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 5kc0 is ON HOLD

Authors: Karpowich, N.K., Wang, D.N., Song, J.M.

Description: Crystal structure of TmRibU, hexagonal crystal form
[[Category: Unreleased Structures]]
[[Category: Song, J.M]]
[[Category: Wang, D.N]]
[[Category: Karpowich, N.K]]