6abp - Revision history

OCA at 14:17, 13 March 2024

OCA — Wed, 13 Mar 2024 14:17:31 GMT

←Older revision		Revision as of 14:17, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6abp' size='340' side='right'caption='[[6abp]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='6abp' size='340' side='right'caption='[[6abp]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ABP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ABP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</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]] 1.67Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [~~http~~://pdbe.org/6abp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6abp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6abp ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</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=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [https://pdbe.org/6abp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [https://www.ebi.ac.uk/pdbsum/6abp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6abp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ARAF_ECOLI ARAF_ECOLI]] Involved in the high-affinity L-arabinose membrane transport system. Binds with high affinity to arabinose, but can also bind D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction).	+	[https://www.uniprot.org/uniprot/ARAF_ECOLI ARAF_ECOLI] Involved in the high-affinity L-arabinose membrane transport system. Binds with high affinity to arabinose, but can also bind D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=6abp ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=6abp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In addition to hydrogen bonds, van der Waals forces contribute to the affinity of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the complexes of the L-arabinose-binding protein (ABP) with monosaccharides have been studied by means of site-directed mutagenesis, equilibrium and rapid kinetic binding techniques, and X-ray crystallography. ABP, a periplasmic transport receptor of Escherichia coli, binds L-arabinose, D-galactose, and D-fucose with preferential affinity in the order of Ara greater than Gal much greater than Fuc. Well-refined, high-resolution structures of ABP complexed with the three sugars revealed that the structural differences in the ABP-sugar complexes are localized around C5 of the sugars, where the equatorial H of Ara has been substituted for CH3 (Fuc) or CH2OH (Gal). The side chain of Met108 undergoes a sterically dictated, ligand-specific, conformational change to optimize nonpolar interactions between its methyl group and the sugar. We found that the Met108Leu ABP binds Gal tighter than wild-type ABP binds Ara and exhibits a preference for ligand in the order of Gal much greater than Fuc greater than Ara. The differences in affinity can be attributed to differences in the dissociation rates of the ABP-sugar complexes. We have refined at better than 1.7-A resolution the crystal structures of the Met108Leu ABP complexed with each of the sugars and offer a molecular explanation for the altered binding properties.
-
-	Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity.,Vermersch PS, Lemon DD, Tesmer JJ, Quiocho FA Biochemistry. 1991 Jul 16;30(28):6861-6. PMID:2069949<ref>PMID:2069949</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6abp" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Quiocho~~, F A~~]]	+	[[Category: Quiocho FA]]
-	[[Category: Tesmer~~, J J.G~~]]	+	[[Category: Tesmer JJG]]
-	[[Category: Vermersch~~, P S]]~~	+	[[Category: Vermersch PS]]
-	~~[[Category: Binding protein~~]]	+

OCA at 21:27, 28 October 2020

OCA — Wed, 28 Oct 2020 21:27:43 GMT

←Older revision		Revision as of 21:27, 28 October 2020
Line 1:		Line 1:
		+
	==SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY==		==SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY==
-	<StructureSection load='6abp' size='340' side='right' caption='[[6abp]], [[Resolution\|resolution]] 1.67Å' scene=''>	+	<StructureSection load='6abp' size='340' side='right'caption='[[6abp]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ABP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ABP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</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=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://pdbe.org/6abp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [http://www.ebi.ac.uk/pdbsum/6abp PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://pdbe.org/6abp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [http://www.ebi.ac.uk/pdbsum/6abp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6abp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ab/6abp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ab/6abp_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Quiocho, F A]]		[[Category: Quiocho, F A]]
	[[Category: Tesmer, J J.G]]		[[Category: Tesmer, J J.G]]
	[[Category: Vermersch, P S]]		[[Category: Vermersch, P S]]
	[[Category: Binding protein]]		[[Category: Binding protein]]

OCA at 02:56, 8 February 2016

OCA — Mon, 08 Feb 2016 02:56:39 GMT

←Older revision		Revision as of 02:56, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='6abp' size='340' side='right' caption='[[6abp]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='6abp' size='340' side='right' caption='[[6abp]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</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=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [http://www.ebi.ac.uk/pdbsum/6abp 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=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://pdbe.org/6abp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [http://www.ebi.ac.uk/pdbsum/6abp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=6abp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 6abp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Quiocho, F A]]		[[Category: Quiocho, F A]]
	[[Category: Tesmer, J J.G]]		[[Category: Tesmer, J J.G]]
	[[Category: Vermersch, P S]]		[[Category: Vermersch, P S]]
	[[Category: Binding protein]]		[[Category: Binding protein]]

OCA at 20:04, 24 December 2014

OCA — Wed, 24 Dec 2014 20:04:39 GMT

←Older revision		Revision as of 20:04, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABP FirstGlance]. <br>		<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [http://www.ebi.ac.uk/pdbsum/6abp 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=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [http://www.ebi.ac.uk/pdbsum/6abp PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ARAF_ECOLI ARAF_ECOLI]] Involved in the high-affinity L-arabinose membrane transport system. Binds with high affinity to arabinose, but can also bind D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Quiocho, F A.]]	+	[[Category: Quiocho, F A]]
-	[[Category: Tesmer, J J.G.]]	+	[[Category: Tesmer, J J.G]]
-	[[Category: Vermersch, P S.]]	+	[[Category: Vermersch, P S]]
	[[Category: Binding protein]]		[[Category: Binding protein]]

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

OCA — Thu, 05 Jun 2014 08:06:05 GMT

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

←Older revision

Revision as of 08:06, 5 June 2014

OCA at 08:06, 5 June 2014

OCA — Thu, 05 Jun 2014 08:06:03 GMT

←Older revision		Revision as of 08:06, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY==
-	[[~~Image~~:6abp.~~png\|left~~\|200px]]	+	<StructureSection load='6abp' size='340' side='right' caption='[[6abp]], [[Resolution\|resolution]] 1.67Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6abp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB], [http://www.ebi.ac.uk/pdbsum/6abp PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ab/6abp_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In addition to hydrogen bonds, van der Waals forces contribute to the affinity of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the complexes of the L-arabinose-binding protein (ABP) with monosaccharides have been studied by means of site-directed mutagenesis, equilibrium and rapid kinetic binding techniques, and X-ray crystallography. ABP, a periplasmic transport receptor of Escherichia coli, binds L-arabinose, D-galactose, and D-fucose with preferential affinity in the order of Ara greater than Gal much greater than Fuc. Well-refined, high-resolution structures of ABP complexed with the three sugars revealed that the structural differences in the ABP-sugar complexes are localized around C5 of the sugars, where the equatorial H of Ara has been substituted for CH3 (Fuc) or CH2OH (Gal). The side chain of Met108 undergoes a sterically dictated, ligand-specific, conformational change to optimize nonpolar interactions between its methyl group and the sugar. We found that the Met108Leu ABP binds Gal tighter than wild-type ABP binds Ara and exhibits a preference for ligand in the order of Gal much greater than Fuc greater than Ara. The differences in affinity can be attributed to differences in the dissociation rates of the ABP-sugar complexes. We have refined at better than 1.7-A resolution the crystal structures of the Met108Leu ABP complexed with each of the sugars and offer a molecular explanation for the altered binding properties.

-	<!--	+	Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity.,Vermersch PS, Lemon DD, Tesmer JJ, Quiocho FA Biochemistry. 1991 Jul 16;30(28):6861-6. PMID:2069949<ref>PMID:2069949</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_6abp"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_6abp\| PDB=6abp \| SCENE= }}~~	+

-	~~===SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_2069949}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 2069949 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_2069949}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~6ABP is a 1 chain structure of sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:2069949<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Quiocho, F A.]]		[[Category: Quiocho, F A.]]
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	[[Category: Vermersch, P S.]]		[[Category: Vermersch, P S.]]
	[[Category: Binding protein]]		[[Category: Binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:17:40 2009''

OCA at 16:17, 16 February 2009

OCA — Mon, 16 Feb 2009 16:17:41 GMT

←Older revision		Revision as of 16:17, 16 February 2009
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	==About this Structure==		==About this Structure==
-	6ABP is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA].	+	6ABP is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABP OCA].

	==Reference==		==Reference==
-	Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity., Vermersch PS, Lemon DD, Tesmer JJ, Quiocho FA, Biochemistry. 1991 Jul 16;30(28):6861-6. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/2069949 2069949]~~	+	<ref group="xtra">PMID:2069949</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Quiocho, F A.]]		[[Category: Quiocho, F A.]]
	[[Category: Tesmer, J J.G.]]		[[Category: Tesmer, J J.G.]]
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	[[Category: Binding protein]]		[[Category: Binding protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14~~:14:~~03 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:17:40 2009''

OCA at 11:14, 3 July 2008

OCA — Thu, 03 Jul 2008 11:14:03 GMT

←Older revision		Revision as of 11:14, 3 July 2008
Line 1:		Line 1:
-	[[Image:6abp.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:6abp.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_6abp\| PDB=6abp \| SCENE= }}		{{STRUCTURE_6abp\| PDB=6abp \| SCENE= }}

-	~~'''~~SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY~~'''~~	+	===SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY===


-	~~==Overview==~~	+	<!--
-	~~In addition to hydrogen bonds~~, ~~van der Waals forces contribute~~ to the ~~affinity of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the complexes of the L-arabinose-binding protein~~ (~~ABP) with monosaccharides have been studied by means of site-directed mutagenesis, equilibrium and rapid kinetic binding techniques, and X-ray crystallography~~. ~~ABP, a periplasmic transport receptor of Escherichia coli, binds L-arabinose, D-galactose, and D-fucose with preferential affinity in the order of Ara greater than Gal much greater than Fuc~~. ~~Well-refined, high-resolution structures of ABP complexed with the three sugars revealed that the structural differences in the ABP-sugar complexes are localized around C5 of the sugars~~, where the ~~equatorial H of Ara has been substituted for CH3 (Fuc) or CH2OH (Gal)~~. ~~The side chain of Met108 undergoes a sterically dictated, ligand~~-~~specific, conformational change to optimize nonpolar interactions between its methyl group and the sugar. We found that the Met108Leu ABP binds Gal tighter than wild~~-type ABP binds Ara and exhibits a preference for ligand in the order of Gal much greater than Fuc greater than Ara. The differences in affinity can be attributed to differences in the dissociation rates of the ABP-sugar complexes. We have refined at better than 1.7-A resolution the crystal structures of the Met108Leu ABP complexed with each of the sugars and offer a molecular explanation for the altered binding properties.	+	The line below this paragraph, {{ABSTRACT_PUBMED_2069949}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 2069949 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_2069949}}

	==About this Structure==		==About this Structure==
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	[[Category: Vermersch, P S.]]		[[Category: Vermersch, P S.]]
	[[Category: Binding protein]]		[[Category: Binding protein]]
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		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 14:14:03 2008''

OCA at 19:38, 4 May 2008

OCA — Sun, 04 May 2008 19:38:52 GMT

←Older revision		Revision as of 19:38, 4 May 2008
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	[[Image:6abp.gif\|left\|200px]]		[[Image:6abp.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 6abp \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>6abp</scene>~~, ~~resolution 1~~.~~67Å~~	+	The line below this paragraph, containing "STRUCTURE_6abp", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=ARA:ALPHA~~-L-~~ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</scene~~>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_6abp\| PDB=6abp \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://www.ebi.ac.uk/pdbsum/6abp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB]</span>	+
-	}}	+

	'''SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY'''		'''SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY'''
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	[[Category: Tesmer, J J.G.]]		[[Category: Tesmer, J J.G.]]
	[[Category: Vermersch, P S.]]		[[Category: Vermersch, P S.]]
-	[[Category: ~~binding~~ protein]]	+	[[Category: Binding protein]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:38:50 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:42:32 2008''	+

OCA at 02:42, 31 March 2008

OCA — Mon, 31 Mar 2008 02:42:35 GMT

←Older revision		Revision as of 02:42, 31 March 2008
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	\|PDB= 6abp \|SIZE=350\|CAPTION= <scene name='initialview01'>6abp</scene>, resolution 1.67Å		\|PDB= 6abp \|SIZE=350\|CAPTION= <scene name='initialview01'>6abp</scene>, resolution 1.67Å
	\|SITE=		\|SITE=
-	\|LIGAND=	+	\|LIGAND= <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=ARB:BETA-L-ARABINOSE'>ARB</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6abp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abp OCA], [http://www.ebi.ac.uk/pdbsum/6abp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=6abp RCSB]</span>
	}}		}}

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	[[Category: binding protein]]		[[Category: binding protein]]

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