5owf - Revision history

OCA at 01:26, 28 December 2023

OCA — Thu, 28 Dec 2023 01:26:34 GMT

←Older revision		Revision as of 01:26, 28 December 2023
Line 1:		Line 1:

	==Structure of a LAO-binding protein mutant with glutamine==		==Structure of a LAO-binding protein mutant with glutamine==
-	<StructureSection load='5owf' size='340' side='right' caption='[[5owf]], [[Resolution\|resolution]] 1.91Å' scene=''>	+	<StructureSection load='5owf' size='340' side='right'caption='[[5owf]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5owf]] 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=5OWF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OWF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5owf]] 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=5OWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OWF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.91Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5owf OCA], [~~http~~://pdbe.org/5owf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5owf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5owf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5owf 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=5owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5owf OCA], [https://pdbe.org/5owf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5owf RCSB], [https://www.ebi.ac.uk/pdbsum/5owf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5owf 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 ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Salty~~]]	+	[[Category: Large Structures]]
-	[[Category: Banda-Vazquez, J]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	[[Category: Hocker, B]]	+	[[Category: Banda-Vazquez J]]
-	[[Category: Shanmugaratnam, S]]	+	[[Category: Hocker B]]
-	[[Category: Sosa-Peinado, A]]	+	[[Category: Shanmugaratnam S]]
-	~~[[Category: Binding pocket]]~~	+	[[Category: Sosa-Peinado A]]
-	~~[[Category: Ligand specificity]]~~	+
-	~~[[Category: Periplasmatic binding protein]]~~	+
-	~~[[Category: Protein design]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 05:52, 25 April 2018

OCA — Wed, 25 Apr 2018 05:52:51 GMT

←Older revision		Revision as of 05:52, 25 April 2018
Line 3:		Line 3:
	<StructureSection load='5owf' size='340' side='right' caption='[[5owf]], [[Resolution\|resolution]] 1.91Å' scene=''>		<StructureSection load='5owf' size='340' side='right' caption='[[5owf]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5owf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OWF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OWF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5owf]] 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=5OWF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OWF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=~~28901 "Bacillus cholerae-suis" Smith 1894~~])</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=5owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5owf OCA], [http://pdbe.org/5owf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5owf RCSB], [http://www.ebi.ac.uk/pdbsum/5owf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5owf 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=5owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5owf OCA], [http://pdbe.org/5owf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5owf RCSB], [http://www.ebi.ac.uk/pdbsum/5owf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5owf ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus cholerae-suis smith 1894~~]]	+	[[Category: Salty]]
	[[Category: Banda-Vazquez, J]]		[[Category: Banda-Vazquez, J]]
	[[Category: Hocker, B]]		[[Category: Hocker, B]]

OCA at 06:29, 18 April 2018

OCA — Wed, 18 Apr 2018 06:29:24 GMT

←Older revision		Revision as of 06:29, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='5owf' size='340' side='right' caption='[[5owf]], [[Resolution\|resolution]] 1.91Å' scene=''>		<StructureSection load='5owf' size='340' side='right' caption='[[5owf]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5owf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OWF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OWF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5owf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OWF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OWF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=28901 "Bacillus cholerae-suis" Smith 1894])</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=5owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5owf OCA], [http://pdbe.org/5owf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5owf RCSB], [http://www.ebi.ac.uk/pdbsum/5owf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5owf 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=5owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5owf OCA], [http://pdbe.org/5owf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5owf RCSB], [http://www.ebi.ac.uk/pdbsum/5owf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5owf ProSAT]</span></td></tr>
	</table>		</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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus cholerae-suis smith 1894]]
	[[Category: Banda-Vazquez, J]]		[[Category: Banda-Vazquez, J]]
	[[Category: Hocker, B]]		[[Category: Hocker, B]]

OCA at 07:31, 21 March 2018

OCA — Wed, 21 Mar 2018 07:31:44 GMT

←Older revision		Revision as of 07:31, 21 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5owf is ~~ON HOLD until Paper~~ Publication	+	==Structure of a LAO-binding protein mutant with glutamine==
		+	<StructureSection load='5owf' size='340' side='right' caption='[[5owf]], [[Resolution\|resolution]] 1.91Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5owf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OWF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OWF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5owf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5owf OCA], [http://pdbe.org/5owf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5owf RCSB], [http://www.ebi.ac.uk/pdbsum/5owf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5owf ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Computational protein design is still a challenge for advancing structure-function relationships. While recent advances in this field are promising, more information for genuine predictions is needed. Here, we discuss different approaches applied to install novel glutamine (Gln) binding into the Lysine/Arginine/Ornithine binding protein (LAOBP) from Salmonella typhimurium. We studied the ligand binding behaviour of two mutants: a binding pocket grafting design based on a structural superposition of LAOBP to the Gln binding protein QBP from Escherichia coli and a design based on statistical coupled positions. The latter showed the ability to bind Gln even though the protein was not very stable. Comparison of both approaches highlighted a non-conservative shared point mutation between LAOBP_graft and LAOBP_sca. This context dependent L117K mutation in LAOBP turned out to be sufficient for introducing Gln binding, as confirmed by different experimental techniques. Moreover, the crystal structure of LAOBP_L117K in complex with its ligand is reported. This article is protected by copyright. All rights reserved.

-	~~Authors~~:	+	Redesign of LAOBP to bind novel L-amino acid ligands.,Banda-Vazquez J, Shanmugaratnam S, Rodriguez-Sotres R, Torres-Larios A, Hocker B, Sosa-Peinado A Protein Sci. 2018 Mar 10. doi: 10.1002/pro.3403. PMID:29524280<ref>PMID:29524280</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5owf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Banda-Vazquez, J]]
		+	[[Category: Hocker, B]]
		+	[[Category: Shanmugaratnam, S]]
		+	[[Category: Sosa-Peinado, A]]
		+	[[Category: Binding pocket]]
		+	[[Category: Ligand specificity]]
		+	[[Category: Periplasmatic binding protein]]
		+	[[Category: Protein design]]
		+	[[Category: Transport protein]]

OCA: Protected "5owf" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:55:51 GMT

Protected "5owf" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:55, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5owf is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 12:55:50 GMT

New page: '''Unreleased structure''' The entry 5owf is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5owf is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]