7qoa - Revision history

OCA at 13:20, 1 February 2024

OCA — Thu, 01 Feb 2024 13:20:23 GMT

←Older revision		Revision as of 13:20, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7qoa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qoa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A6L:2,3-dihydroxypropyl+(9Z)-octadec-9-enoate'>A6L</scene>, <scene name='pdbligand=CYT:6-AMINOPYRIMIDIN-2(1H)-ONE'>CYT</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEF:DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE'>PEF</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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A6L:2,3-dihydroxypropyl+(9Z)-octadec-9-enoate'>A6L</scene>, <scene name='pdbligand=CYT:6-AMINOPYRIMIDIN-2(1H)-ONE'>CYT</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEF:DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE'>PEF</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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa 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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A857SHB2_PROVU A0A857SHB2_PROVU]]	+	[https://www.uniprot.org/uniprot/A0A857SHB2_PROVU A0A857SHB2_PROVU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 05:46, 8 September 2022

OCA — Thu, 08 Sep 2022 05:46:20 GMT

←Older revision		Revision as of 05:46, 8 September 2022
Line 1:		Line 1:

	==Structure of CodB, a cytosine transporter in an outward-facing conformation==		==Structure of CodB, a cytosine transporter in an outward-facing conformation==
-	<StructureSection load='7qoa' size='340' side='right'caption='[[7qoa]]' scene=''>	+	<StructureSection load='7qoa' size='340' side='right'caption='[[7qoa]], [[Resolution\|resolution]] 2.40Å' 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=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7qoa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA 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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa 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=A6L:2,3-dihydroxypropyl+(9Z)-octadec-9-enoate'>A6L</scene>, <scene name='pdbligand=CYT:6-AMINOPYRIMIDIN-2(1H)-ONE'>CYT</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEF:DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE'>PEF</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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A857SHB2_PROVU A0A857SHB2_PROVU]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CodB is a cytosine transporter from the Nucleobase-Cation-Symport-1 (NCS1) transporter family, a member of the widespread LeuT superfamily. Previous experiments with the nosocomial pathogen Pseudomonas aeruginosa have shown CodB as also important for the uptake of 5-fluorocytosine, which has been suggested as a novel drug to combat antimicrobial resistance by suppressing virulence. Here we solve the crystal structure of CodB from Proteus vulgaris, at 2.4 A resolution in complex with cytosine. We show that CodB carries out the sodium-dependent uptake of cytosine and can bind 5-fluorocytosine. Comparison of the substrate-bound structures of CodB and the hydantoin transporter Mhp1, the only other NCS1 family member for which the structure is known, highlight the importance of the hydrogen bonds that the substrates make with the main chain at the breakpoint in the discontinuous helix, TM6. In contrast to other LeuT superfamily members, neither CodB nor Mhp1 makes specific interactions with residues on TM1. Comparison of the structures provides insight into the intricate mechanisms of how these proteins transport substrates across the plasma membrane.
		+
		+	Structure of cytosine transport protein CodB provides insight into nucleobase-cation symporter 1 mechanism.,Hatton CE, Brotherton DH, Spencer M, Cameron AD EMBO J. 2022 Jul 1:e110527. doi: 10.15252/embj.2021110527. PMID:35775318<ref>PMID:35775318</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7qoa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Proteus vulgaris]]
	[[Category: Cameron AD]]		[[Category: Cameron AD]]
	[[Category: Hatton CE]]		[[Category: Hatton CE]]

OCA at 11:05, 31 August 2022

OCA — Wed, 31 Aug 2022 11:05:12 GMT

←Older revision		Revision as of 11:05, 31 August 2022
Line 1:		Line 1:

	==Structure of CodB, a cytosine transporter in an outward-facing conformation==		==Structure of CodB, a cytosine transporter in an outward-facing conformation==
-	<StructureSection load='7qoa' size='340' side='right'caption='[[7qoa]]~~, [[Resolution\|resolution]] 2.40Å~~' scene=''>	+	<StructureSection load='7qoa' size='340' side='right'caption='[[7qoa]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7qoa]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A6L:2,3-dihydroxypropyl+(9Z)-octadec-9-enoate'>A6L</scene>, <scene name='pdbligand=CYT:6-AMINOPYRIMIDIN-2(1H)-ONE'>CYT</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEF:DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE'>PEF</scene></td></tr>	+	</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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa 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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	CodB is a cytosine transporter from the Nucleobase-Cation-Symport-1 (NCS1) transporter family, a member of the widespread LeuT superfamily. Previous experiments with the nosocomial pathogen Pseudomonas aeruginosa have shown CodB as also important for the uptake of 5-fluorocytosine, which has been suggested as a novel drug to combat antimicrobial resistance by suppressing virulence. Here we solve the crystal structure of CodB from Proteus vulgaris, at 2.4 A resolution in complex with cytosine. We show that CodB carries out the sodium-dependent uptake of cytosine and can bind 5-fluorocytosine. Comparison of the substrate-bound structures of CodB and the hydantoin transporter Mhp1, the only other NCS1 family member for which the structure is known, highlight the importance of the hydrogen bonds that the substrates make with the main chain at the breakpoint in the discontinuous helix, TM6. In contrast to other LeuT superfamily members, neither CodB nor Mhp1 makes specific interactions with residues on TM1. Comparison of the structures provides insight into the intricate mechanisms of how these proteins transport substrates across the plasma membrane.
-
-	Structure of cytosine transport protein CodB provides insight into nucleobase-cation symporter 1 mechanism.,Hatton CE, Brotherton DH, Spencer M, Cameron AD EMBO J. 2022 Jul 1:e110527. doi: 10.15252/embj.2021110527. PMID:35775318<ref>PMID:35775318</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7qoa" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cameron~~, A D~~]]	+	[[Category: Cameron AD]]
-	[[Category: Hatton~~, C E]]~~	+	[[Category: Hatton CE]]
-	~~[[Category: Cytosine]]~~	+
-	~~[[Category: Membrane transporter]]~~	+
-	~~[[Category: Sodium]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 05:12, 25 August 2022

OCA — Thu, 25 Aug 2022 05:12:14 GMT

←Older revision		Revision as of 05:12, 25 August 2022
Line 1:		Line 1:

	==Structure of CodB, a cytosine transporter in an outward-facing conformation==		==Structure of CodB, a cytosine transporter in an outward-facing conformation==
-	<StructureSection load='7qoa' size='340' side='right'caption='[[7qoa]]' scene=''>	+	<StructureSection load='7qoa' size='340' side='right'caption='[[7qoa]], [[Resolution\|resolution]] 2.40Å' 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=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7qoa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA 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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa 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=A6L:2,3-dihydroxypropyl+(9Z)-octadec-9-enoate'>A6L</scene>, <scene name='pdbligand=CYT:6-AMINOPYRIMIDIN-2(1H)-ONE'>CYT</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEF:DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE'>PEF</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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CodB is a cytosine transporter from the Nucleobase-Cation-Symport-1 (NCS1) transporter family, a member of the widespread LeuT superfamily. Previous experiments with the nosocomial pathogen Pseudomonas aeruginosa have shown CodB as also important for the uptake of 5-fluorocytosine, which has been suggested as a novel drug to combat antimicrobial resistance by suppressing virulence. Here we solve the crystal structure of CodB from Proteus vulgaris, at 2.4 A resolution in complex with cytosine. We show that CodB carries out the sodium-dependent uptake of cytosine and can bind 5-fluorocytosine. Comparison of the substrate-bound structures of CodB and the hydantoin transporter Mhp1, the only other NCS1 family member for which the structure is known, highlight the importance of the hydrogen bonds that the substrates make with the main chain at the breakpoint in the discontinuous helix, TM6. In contrast to other LeuT superfamily members, neither CodB nor Mhp1 makes specific interactions with residues on TM1. Comparison of the structures provides insight into the intricate mechanisms of how these proteins transport substrates across the plasma membrane.
		+
		+	Structure of cytosine transport protein CodB provides insight into nucleobase-cation symporter 1 mechanism.,Hatton CE, Brotherton DH, Spencer M, Cameron AD EMBO J. 2022 Jul 1:e110527. doi: 10.15252/embj.2021110527. PMID:35775318<ref>PMID:35775318</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7qoa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cameron AD]]	+	[[Category: Cameron, A D]]
-	[[Category: Hatton CE]]	+	[[Category: Hatton, C E]]
		+	[[Category: Cytosine]]
		+	[[Category: Membrane transporter]]
		+	[[Category: Sodium]]
		+	[[Category: Transport protein]]

OCA at 05:15, 13 July 2022

OCA — Wed, 13 Jul 2022 05:15:16 GMT

←Older revision		Revision as of 05:15, 13 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7qoa ~~is ON HOLD until Paper Publication~~	+	==Structure of CodB, a cytosine transporter in an outward-facing conformation==
-		+	<StructureSection load='7qoa' size='340' side='right'caption='[[7qoa]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOA 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=7qoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qoa OCA], [https://pdbe.org/7qoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qoa RCSB], [https://www.ebi.ac.uk/pdbsum/7qoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qoa ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cameron AD]]
		+	[[Category: Hatton CE]]

OCA at 08:57, 16 February 2022

OCA — Wed, 16 Feb 2022 08:57:30 GMT

←Older revision		Revision as of 08:57, 16 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 29 Dec 2021 11:58:46 GMT

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

←Older revision

Revision as of 11:58, 29 December 2021

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

OCA — Wed, 29 Dec 2021 11:58:44 GMT

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

New page

'''Unreleased structure'''

The entry 7qoa is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]