7rcp - Revision history

OCA at 07:33, 3 November 2022

2022-11-03T07:33:21Z

←Older revision		Revision as of 07:33, 3 November 2022
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	==GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions==		==GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions==
-	<StructureSection load='7rcp' size='340' side='right'caption='[[7rcp]]' scene=''>	+	<StructureSection load='7rcp' size='340' side='right'caption='[[7rcp]], [[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=7RCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RCP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rcp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RCP 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=7rcp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rcp OCA], [https://pdbe.org/7rcp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rcp RCSB], [https://www.ebi.ac.uk/pdbsum/7rcp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rcp 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=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7rcp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rcp OCA], [https://pdbe.org/7rcp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rcp RCSB], [https://www.ebi.ac.uk/pdbsum/7rcp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rcp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GLT_PYRHO GLT_PYRHO] Sodium-dependent, high-affinity amino acid transporter that mediates aspartate uptake (PubMed:17435767, PubMed:19380583, PubMed:17230192, Ref.11). Has only very low glutamate transport activity (PubMed:19380583, PubMed:17230192). Functions as a symporter that transports one amino acid molecule together with two or three Na(+) ions, resulting in electrogenic transport (PubMed:17435767, PubMed:19380583, Ref.11). Na(+) binding enhances the affinity for aspartate (PubMed:19380583, Ref.11). Mediates Cl(-) flux that is not coupled to amino acid transport; this avoids the accumulation of negative charges due to aspartate and Na(+) symport (PubMed:17435767). In contrast to mammalian homologs, transport does not depend on pH or K(+) ions (PubMed:19380583).<ref>PMID:17230192</ref> <ref>PMID:17435767</ref> <ref>PMID:19380583</ref> [PDB:4P19]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Integral membrane glutamate transporters couple the concentrative substrate transport to ion gradients. There is a wealth of structural and mechanistic information about this protein family. Recent studies of an archaeal homologue, GltPh, revealed transport rate heterogeneity, which is inconsistent with simple kinetic models; however, its structural and mechanistic determinants remain undefined. Here, we demonstrate that in a mutant GltPh, which exclusively populates the outward-facing state, at least two substates coexist in slow equilibrium, binding the substrate with different apparent affinities. Wild type GltPh shows similar binding properties, and modulation of the substate equilibrium correlates with transport rates. The low-affinity substate of the mutant is transient following substrate binding. Consistently, cryo-EM on samples frozen within seconds after substrate addition reveals the presence of structural classes with perturbed helical packing of the extracellular half of the transport domain in regions adjacent to the binding site. By contrast, an equilibrated structure does not show such classes. The structure at 2.2-A resolution details a pattern of waters in the intracellular half of the domain and resolves classes with subtle differences in the substrate-binding site. We hypothesize that the rigid cytoplasmic half of the domain mediates substrate and ion recognition and coupling, whereas the extracellular labile half sets the affinity and dynamic properties.
		+
		+	The archaeal glutamate transporter homologue GltPh shows heterogeneous substrate binding.,Reddy KD, Ciftci D, Scopelliti AJ, Boudker O J Gen Physiol. 2022 May 2;154(5). pii: 213177. doi: 10.1085/jgp.202213131. Epub, 2022 Apr 22. PMID:35452090<ref>PMID:35452090</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7rcp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pyrococcus horikoshii OT3]]
	[[Category: Boudker O]]		[[Category: Boudker O]]
	[[Category: Reddy KD]]		[[Category: Reddy KD]]

OCA at 02:55, 21 April 2022

2022-04-21T02:55:54Z

←Older revision		Revision as of 02:55, 21 April 2022
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-	'''Unreleased structure'''

-	~~The entry 7rcp is ON HOLD until Paper Publication~~	+	==GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions==
-		+	<StructureSection load='7rcp' size='340' side='right'caption='[[7rcp]]' scene=''>
-	~~Authors: Reddy, K.D., Boudker, O.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RCP FirstGlance]. <br>
-	~~Description:~~ GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions	+	</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=7rcp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rcp OCA], [https://pdbe.org/7rcp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rcp RCSB], [https://www.ebi.ac.uk/pdbsum/7rcp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rcp ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Reddy~~, K.D]]	+	__TOC__
-	[[Category: Boudker, O]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Boudker O]]
		+	[[Category: Reddy KD]]

OCA at 05:05, 18 August 2021

2021-08-18T05:05:14Z

←Older revision		Revision as of 05:05, 18 August 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Reddy, K.D., Boudker, O.		Authors: Reddy, K.D., Boudker, O.
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	Description: GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions		Description: GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Boudker, O]]
	[[Category: Reddy, K.D]]		[[Category: Reddy, K.D]]
		+	[[Category: Boudker, O]]

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

2021-07-14T08:58:06Z

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

←Older revision

Revision as of 08:58, 14 July 2021

OCA: New page: '''Unreleased structure''' The entry 7rcp is ON HOLD Authors: Reddy, K.D., Boudker, O. Description: GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions [[Category: Unr...

2021-07-14T08:58:05Z

New page: '''Unreleased structure''' The entry 7rcp is ON HOLD Authors: Reddy, K.D., Boudker, O. Description: GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions [[Category: Unr...

New page

'''Unreleased structure'''

The entry 7rcp is ON HOLD

Authors: Reddy, K.D., Boudker, O.

Description: GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions
[[Category: Unreleased Structures]]
[[Category: Boudker, O]]
[[Category: Reddy, K.D]]