7c0z - Revision history

OCA at 15:48, 29 November 2023

OCA — Wed, 29 Nov 2023 15:48:28 GMT

←Older revision		Revision as of 15:48, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7c0z' size='340' side='right'caption='[[7c0z]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='7c0z' size='340' side='right'caption='[[7c0z]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7c0z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7c0z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C0Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FGO:[(1S,3R,3aR,6aS)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3a,4,6,6a-hexahydrocyclopenta[c]furan-1-yl]methyl+[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]+hydrogen+phosphate'>FGO</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]] 2.2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0379 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FGO:[(1S,3R,3aR,6aS)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3a,4,6,6a-hexahydrocyclopenta[c]furan-1-yl]methyl+[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]+hydrogen+phosphate'>FGO</scene></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=7c0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0z OCA], [https://pdbe.org/7c0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c0z RCSB], [https://www.ebi.ac.uk/pdbsum/7c0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0z 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=7c0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0z OCA], [https://pdbe.org/7c0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c0z RCSB], [https://www.ebi.ac.uk/pdbsum/7c0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0z ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5SLB4_THET8 Q5SLB4_THET8]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7c0z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7c0z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ABC transporter 3D structures\|ABC transporter 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet8~~]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Chandravanshi, M]]	+	[[Category: Chandravanshi M]]
-	[[Category: Kanaujia~~, S P~~]]	+	[[Category: Kanaujia SP]]
-	[[Category: Samanta, R]]	+	[[Category: Samanta R]]
-	~~[[Category: C-di-gmp/amp]]~~	+
-	~~[[Category: Substrate-binding protein]]~~	+
-	~~[[Category: Thermus thermophilus]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Trna synthesis and/or modification]]~~	+
-	~~[[Category: Ugpb]]~~	+
-	~~[[Category: Venus fly-trap mechanism~~]]	+

OCA at 06:16, 18 August 2021

OCA — Wed, 18 Aug 2021 06:16:28 GMT

←Older revision		Revision as of 06:16, 18 August 2021
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	==Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form II)==		==Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form II)==
-	<StructureSection load='7c0z' size='340' side='right'caption='[[7c0z]]' scene=''>	+	<StructureSection load='7c0z' size='340' side='right'caption='[[7c0z]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7c0z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C0Z FirstGlance]. <br>
-	</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=7c0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0z OCA], [https://pdbe.org/7c0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c0z RCSB], [https://www.ebi.ac.uk/pdbsum/7c0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0z ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FGO:[(1S,3R,3aR,6aS)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3a,4,6,6a-hexahydrocyclopenta[c]furan-1-yl]methyl+[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]+hydrogen+phosphate'>FGO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0379 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=7c0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0z OCA], [https://pdbe.org/7c0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c0z RCSB], [https://www.ebi.ac.uk/pdbsum/7c0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0z ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Substrate (or solute)-binding proteins (SBPs) selectively bind the target ligands and deliver them to the ATP-binding cassette (ABC) transport system for their translocation. Irrespective of the different types of ligands, SBPs are structurally conserved. A wealth of structural details of SBPs bound to different types of ligands and the physiological basis of their import are available; however, the uptake mechanism of nucleotides is still deficient. In this study, we elucidated the structural details of an SBP endogenously bound to a novel ligand, a derivative of uridylyl-3'-5'-phospho-guanosine (U3G); thus, we named it a U3G-binding protein (U3GBP). To the best of our knowledge, this is the first report of U3G (and a dinucleotide) binding to the SBP of ABC transport system, and thus, U3GBP is classified as a first member of subcluster D-I SBPs. Thermodynamic data also suggest that U3GBP can bind phospholipid precursor sn-glycerophosphocholine (GPC) at a site other than the active site. Moreover, a combination of mutagenic and structural information reveals that the protein U3GBP follows the well-known 'Venus Fly-trap' mechanism for dinucleotide binding. DATABASES: Structural data are available in RCSB Protein Data Bank under the accession number(s) 7C0F, 7C0K, 7C0L, 7C0O, 7C0R, 7C0S, 7C0T, 7C0U, 7C0V, 7C0W, 7C0X, 7C0Y, 7C0Z, 7C14, 7C15, 7C16, 7C19, and 7C1B.
		+
		+	Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function.,Chandravanshi M, Samanta R, Kanaujia SP FEBS J. 2021 Feb 18. doi: 10.1111/febs.15774. PMID:33599038<ref>PMID:33599038</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7c0z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chandravanshi M]]	+	[[Category: Thet8]]
-	[[Category: Kanaujia SP]]	+	[[Category: Chandravanshi, M]]
-	[[Category: Samanta R]]	+	[[Category: Kanaujia, S P]]
		+	[[Category: Samanta, R]]
		+	[[Category: C-di-gmp/amp]]
		+	[[Category: Substrate-binding protein]]
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Transport protein]]
		+	[[Category: Trna synthesis and/or modification]]
		+	[[Category: Ugpb]]
		+	[[Category: Venus fly-trap mechanism]]

OCA at 17:17, 10 March 2021

OCA — Wed, 10 Mar 2021 17:17:46 GMT

←Older revision		Revision as of 17:17, 10 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7c0z is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form II)==
-		+	<StructureSection load='7c0z' size='340' side='right'caption='[[7c0z]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C0Z FirstGlance]. <br>
-	~~Description~~:	+	</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=7c0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0z OCA], [https://pdbe.org/7c0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c0z RCSB], [https://www.ebi.ac.uk/pdbsum/7c0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0z ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chandravanshi M]]
		+	[[Category: Kanaujia SP]]
		+	[[Category: Samanta R]]

OCA at 07:25, 9 September 2020

OCA — Wed, 09 Sep 2020 07:25:56 GMT

←Older revision		Revision as of 07:25, 9 September 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7c0z is ON HOLD	+	The entry 7c0z is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7c0z" [edit=sysop:move=sysop]

OCA — Wed, 13 May 2020 04:22:44 GMT

Protected "7c0z" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:22, 13 May 2020

OCA: New page: '''Unreleased structure''' The entry 7c0z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 May 2020 04:22:43 GMT

New page: '''Unreleased structure''' The entry 7c0z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7c0z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]