4xz6 - Revision history

OCA at 17:59, 26 April 2023

OCA — Wed, 26 Apr 2023 17:59:19 GMT

←Older revision		Revision as of 17:59, 26 April 2023
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	<StructureSection load='4xz6' size='340' side='right'caption='[[4xz6]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4xz6' size='340' side='right'caption='[[4xz6]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xz6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ruepo Ruepo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZ6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XZ6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xz6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_pomeroyi_DSS-3 Ruegeria pomeroyi DSS-3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XZ6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPO1548 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246200 RUEPO])~~</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=4xz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xz6 OCA], [https://pdbe.org/4xz6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xz6 RCSB], [https://www.ebi.ac.uk/pdbsum/4xz6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xz6 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=4xz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xz6 OCA], [~~http~~://pdbe.org/4xz6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xz6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xz6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xz6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5LT66_RUEPO Q5LT66_RUEPO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ruepo~~]]	+	[[Category: Ruegeria pomeroyi DSS-3]]
-	[[Category: Li~~, C Y~~]]	+	[[Category: Li CY]]
-	[[Category: Zhang~~, Y Z]]~~	+	[[Category: Zhang YZ]]
-	~~[[Category: Abc transporter]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Substrate binding protein]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 23:52, 5 June 2019

OCA — Wed, 05 Jun 2019 23:52:37 GMT

←Older revision		Revision as of 23:52, 5 June 2019
Line 1:		Line 1:
		+
	==TmoX in complex with TMAO==		==TmoX in complex with TMAO==
-	<StructureSection load='4xz6' size='340' side='right' caption='[[4xz6]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4xz6' size='340' side='right'caption='[[4xz6]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xz6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZ6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xz6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruepo Ruepo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZ6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xz6 OCA], [http://pdbe.org/4xz6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xz6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xz6 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPO1548 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246200 RUEPO])</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=4xz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xz6 OCA], [http://pdbe.org/4xz6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xz6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xz6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xz6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ruepo]]
	[[Category: Li, C Y]]		[[Category: Li, C Y]]
	[[Category: Zhang, Y Z]]		[[Category: Zhang, Y Z]]

OCA at 20:11, 30 November 2015

OCA — Mon, 30 Nov 2015 20:11:27 GMT

←Older revision		Revision as of 20:11, 30 November 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4xz6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZ6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xz6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZ6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xz6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xz6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xz6 PDBsum]</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=4xz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xz6 OCA], [http://pdbe.org/4xz6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xz6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xz6 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. TMAO can also be metabolized by marine bacteria into volatile methylated amines, the precursors of the greenhouse gas nitrous oxide. However, it was not known how TMAO is recognized and imported by bacteria. Ruegeria pomeroyi DSS-3, a marine Roseobacter, has an ATP-binding cassette transporter, TmoXWV, specific for TMAO. TmoX is the substrate-binding protein of the TmoXWV transporter. In this study, the substrate specificity of TmoX of R. pomeroyi DSS-3 was characterized. We further determined the structure of the TmoX/TMAO complex and studied the TMAO-binding mechanism of TmoX by biochemical, structural, and mutational analyses. A Ca(2+) ion chelated by an extended loop in TmoX was shown to be important for maintaining the stability of TmoX. Molecular dynamics simulations indicate that TmoX can alternate between "open" and "closed" states for binding TMAO. In the substrate-binding pocket, four tryptophan residues interact with the quaternary amine of TMAO by cation-pi interactions, and Glu131 forms a hydrogen bond with the polar oxygen atom of TMAO. The pi-pi stacking interactions between the side chains of Phe and Trp are also essential for TMAO binding. Sequence analysis suggests that the TMAO-binding mechanism of TmoX may have universal significance in marine bacteria, especially in the marine Roseobacter clade. This study sheds light on how marine microorganisms utilize TMAO. IMPORTANCE: Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. The products of TMAO metabolized by bacteria are part of the precursors of the greenhouse gas nitrous oxide. It is unclear how TMAO is recognized and imported by bacteria. TmoX is the substrate-binding protein of a TMAO-specific transporter. Here, the substrate specificity of TmoX of Ruegeria pomeroyi DSS-3 was characterized. The TMAO-binding mechanism of TmoX was studied by biochemical, structural, and mutational analyses. Moreover, our results suggest that the TMAO-binding mechanism may have universal significance in marine bacteria. This study sheds light on how marine microorganisms utilize TMAO and should lead to a better understanding of marine nitrogen cycling.
		+
		+	Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3.,Li CY, Chen XL, Shao X, Wei TD, Wang P, Xie BB, Qin QL, Zhang XY, Su HN, Song XY, Shi M, Zhou BC, Zhang YZ J Bacteriol. 2015 Nov 1;197(21):3378-87. doi: 10.1128/JB.00542-15. Epub 2015 Aug , 17. PMID:26283766<ref>PMID:26283766</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4xz6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:25, 20 August 2015

OCA — Thu, 20 Aug 2015 12:25:42 GMT

←Older revision		Revision as of 12:25, 20 August 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==TmoX in complex with TMAO==
-		+	<StructureSection load='4xz6' size='340' side='right' caption='[[4xz6]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~The entry~~ 4xz6 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4xz6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZ6 FirstGlance]. <br>
-	~~Authors~~: ~~Zhang~~, Y.Z., Li, C.Y.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xz6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xz6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xz6 PDBsum]</span></td></tr>
-	~~Description: TmoX in complex with TMAO~~	+	</table>
-	[[Category: ~~Unreleased Structures~~]]	+	__TOC__
-	[[Category: Zhang, Y.Z]]	+	</StructureSection>
-	[[Category: ~~Li, C.Y~~]]	+	[[Category: Li, C Y]]
		+	[[Category: Zhang, Y Z]]
		+	[[Category: Abc transporter]]
		+	[[Category: Complex]]
		+	[[Category: Substrate binding protein]]
		+	[[Category: Transport protein]]

OCA at 12:31, 25 February 2015

OCA — Wed, 25 Feb 2015 12:31:04 GMT

←Older revision		Revision as of 12:31, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xz6 is ON HOLD	+	The entry 4xz6 is ON HOLD until Paper Publication

	Authors: Zhang, Y.Z., Li, C.Y.		Authors: Zhang, Y.Z., Li, C.Y.

OCA: Protected "4xz6" [edit=sysop:move=sysop]

OCA — Thu, 12 Feb 2015 10:53:52 GMT

Protected "4xz6" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:53, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xz6 is ON HOLD Authors: Zhang, Y.Z., Li, C.Y. Description: TmoX in complex with TMAO Category: Unreleased Structures Category: Zhang, Y.Z ...

OCA — Thu, 12 Feb 2015 10:53:51 GMT

New page: '''Unreleased structure''' The entry 4xz6 is ON HOLD Authors: Zhang, Y.Z., Li, C.Y. Description: TmoX in complex with TMAO Category: Unreleased Structures Category: Zhang, Y.Z ...

New page

'''Unreleased structure'''

The entry 4xz6 is ON HOLD

Authors: Zhang, Y.Z., Li, C.Y.

Description: TmoX in complex with TMAO
[[Category: Unreleased Structures]]
[[Category: Zhang, Y.Z]]
[[Category: Li, C.Y]]