6mku - Revision history

OCA at 06:33, 11 October 2023

OCA — Wed, 11 Oct 2023 06:33:33 GMT

←Older revision		Revision as of 06:33, 11 October 2023
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	<StructureSection load='6mku' size='340' side='right'caption='[[6mku]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='6mku' size='340' side='right'caption='[[6mku]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mku]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salty Salty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MKU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mku]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MKU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.727Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">argT, STM2355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6mku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mku OCA], [~~http~~://pdbe.org/6mku PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mku RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mku PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mku 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=6mku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mku OCA], [https://pdbe.org/6mku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mku RCSB], [https://www.ebi.ac.uk/pdbsum/6mku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mku ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ARGT_SALTY ARGT_SALTY]] This periplasmic binding protein is involved in an arginine transport system. ArgT and histidine-binding protein J (HisJ) interact with a common membrane-bound receptor, HisP.	+	[https://www.uniprot.org/uniprot/ARGT_SALTY ARGT_SALTY] This periplasmic binding protein is involved in an arginine transport system. ArgT and histidine-binding protein J (HisJ) interact with a common membrane-bound receptor, HisP.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Salty~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	[[Category: Espinoza-Perez, G]]	+	[[Category: Espinoza-Perez G]]
-	[[Category: Rodriguez-Romero, A]]	+	[[Category: Rodriguez-Romero A]]
-	[[Category: Romero-Romero, S]]	+	[[Category: Romero-Romero S]]
-	[[Category: Vergara, R]]	+	[[Category: Vergara R]]
-	~~[[Category: Lao]]~~	+
-	~~[[Category: Periplasmic binding protein]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Protein ligand complex]]~~	+
-	~~[[Category: Thermodynamic~~]]	+

OCA at 10:22, 26 February 2020

OCA — Wed, 26 Feb 2020 10:22:34 GMT

←Older revision		Revision as of 10:22, 26 February 2020
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	<StructureSection load='6mku' size='340' side='right'caption='[[6mku]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='6mku' size='340' side='right'caption='[[6mku]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mku]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mku]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">argT, STM2355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=6mku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mku OCA], [http://pdbe.org/6mku PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mku RCSB], [http://www.ebi.ac.uk/pdbsum/6mku PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mku 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=6mku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mku OCA], [http://pdbe.org/6mku PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mku RCSB], [http://www.ebi.ac.uk/pdbsum/6mku PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mku ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Salty]]
	[[Category: Espinoza-Perez, G]]		[[Category: Espinoza-Perez, G]]
	[[Category: Rodriguez-Romero, A]]		[[Category: Rodriguez-Romero, A]]

OCA at 05:53, 7 August 2019

OCA — Wed, 07 Aug 2019 05:53:34 GMT

←Older revision		Revision as of 05:53, 7 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6mku is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with arginine==
		+	<StructureSection load='6mku' size='340' side='right'caption='[[6mku]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6mku]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6mku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mku OCA], [http://pdbe.org/6mku PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mku RCSB], [http://www.ebi.ac.uk/pdbsum/6mku PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mku ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ARGT_SALTY ARGT_SALTY]] This periplasmic binding protein is involved in an arginine transport system. ArgT and histidine-binding protein J (HisJ) interact with a common membrane-bound receptor, HisP.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The study of binding thermodynamics is essential to understand how affinity and selectivity are acquired in molecular complexes. Periplasmic binding proteins (PBPs) are macromolecules of biotechnological interest that bind a broad number of ligands and have been used to design biosensors. The lysine-arginine-ornithine binding protein (LAO) is a PBP of 238 residues that binds the basic amino acids l-arginine and l-histidine with nm and mum affinity, respectively. It has been shown that the affinity difference for arginine and histidine binding is caused by enthalpy, this correlates with the higher number of protein-ligand contacts formed with arginine. In order to elucidate the structural bases that determine binding affinity and selectivity in LAO, the contribution of protein-ligand contacts to binding energetics was assessed. To this end, an alanine scanning of the LAO-binding site residues was performed and arginine and histidine binding were characterized by isothermal titration calorimetry and X-ray crystallography. Although unexpected enthalpy and entropy changes were observed in some mutants, thermodynamic data correlated with structural information, especially, the binding heat capacity change. We found that selectivity is conferred by several residues rather than exclusive arginine-protein interactions. Furthermore, crystallographic structures revealed that protein-ligand contributions to binding thermodynamics are highly influenced by the solvent. Finally, we found a similar backbone conformation in all the closed structures obtained, but different structures in the open state, suggesting that the binding site residues of LAO play an important role in stabilizing not only the holo conformation, but also the apo state. DATABASE: Structural data are available in the Protein Data Bank database under the accession numbers 6MLE, 6MLN, 6MLG, 6MKX, 6MLI, 6MLA, 6MKU, 6MKW, 6ML0, 6MLD, 6MLV, 6MLO, 6MLP, 6ML9, 6MLJ.

-	~~Authors: Romero~~-~~Romero, S~~., Vergara, R., Espinoza-Perez, G., Rodriguez-~~Romero~~, A.	+	The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein.,Vergara R, Romero-Romero S, Velazquez-Lopez I, Espinoza-Perez G, Rodriguez-Hernandez A, Pulido NO, Sosa-Peinado A, Rodriguez-Romero A, Fernandez-Velasco DA FEBS J. 2019 Jul 26. doi: 10.1111/febs.15019. PMID:31348608<ref>PMID:31348608</ref>

-	~~Description: Crystal structure~~ of the ~~periplasmic Lysine~~-~~, Arginine~~-~~, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with arginine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6mku" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Espinoza-Perez, G]]		[[Category: Espinoza-Perez, G]]
-	[[Category: Vergara, R]]
-	[[Category: Romero-Romero, S]]
	[[Category: Rodriguez-Romero, A]]		[[Category: Rodriguez-Romero, A]]
		+	[[Category: Romero-Romero, S]]
		+	[[Category: Vergara, R]]
		+	[[Category: Lao]]
		+	[[Category: Periplasmic binding protein]]
		+	[[Category: Protein binding]]
		+	[[Category: Protein ligand complex]]
		+	[[Category: Thermodynamic]]

OCA at 06:31, 17 October 2018

OCA — Wed, 17 Oct 2018 06:31:46 GMT

←Older revision		Revision as of 06:31, 17 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6mku is ON HOLD	+	The entry 6mku is ON HOLD until Paper Publication

	Authors: Romero-Romero, S., Vergara, R., Espinoza-Perez, G., Rodriguez-Romero, A.		Authors: Romero-Romero, S., Vergara, R., Espinoza-Perez, G., Rodriguez-Romero, A.

OCA: Protected "6mku" [edit=sysop:move=sysop]

OCA — Wed, 03 Oct 2018 06:30:05 GMT

Protected "6mku" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:30, 3 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mku is ON HOLD Authors: Romero-Romero, S., Vergara, R., Espinoza-Perez, G., Rodriguez-Romero, A. Description: Crystal structure of the periplasmic...

OCA — Wed, 03 Oct 2018 06:30:03 GMT

New page: '''Unreleased structure''' The entry 6mku is ON HOLD Authors: Romero-Romero, S., Vergara, R., Espinoza-Perez, G., Rodriguez-Romero, A. Description: Crystal structure of the periplasmic...

New page

'''Unreleased structure'''

The entry 6mku is ON HOLD

Authors: Romero-Romero, S., Vergara, R., Espinoza-Perez, G., Rodriguez-Romero, A.

Description: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with arginine
[[Category: Unreleased Structures]]
[[Category: Espinoza-Perez, G]]
[[Category: Vergara, R]]
[[Category: Romero-Romero, S]]
[[Category: Rodriguez-Romero, A]]