2pug - Revision history

OCA at 09:12, 21 February 2024

2024-02-21T09:12:09Z

←Older revision		Revision as of 09:12, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2pug' size='340' side='right'caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pug' size='340' side='right'caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pug]] is a 2 chain structure with sequence from [https://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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pug]] is a 2 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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</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]] 2.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PURR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [https://pdbe.org/2pug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [https://www.ebi.ac.uk/pdbsum/2pug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pug 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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [https://pdbe.org/2pug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [https://www.ebi.ac.uk/pdbsum/2pug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pug ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PURR_ECOLI PURR_ECOLI]] Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.<ref>PMID:2404765</ref> <ref>PMID:2211500</ref> <ref>PMID:1400170</ref> <ref>PMID:14741201</ref>	+	[https://www.uniprot.org/uniprot/PURR_ECOLI PURR_ECOLI] Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.<ref>PMID:2404765</ref> <ref>PMID:2211500</ref> <ref>PMID:1400170</ref> <ref>PMID:14741201</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		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=2pug 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=2pug ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Guanine or hypoxanthine, physiological corepressors of the Escherichia coli purine repressor (PurR), promote formation of the ternary PurR-corepressor-operator DNA complex that functions to repress pur operon gene expression. Structure-based predictions on the importance of Arg190 in determining 6-oxopurine specificity and corepressor binding affinity were tested by mutagenesis, analysis of in vivo function, and in vitro corepressor binding measurements. Replacements of Arg190 with Ala or Gln resulted in functional repressors in which binding of guanine and hypoxanthine was retained but specificity was relaxed to permit binding of adenine. X-ray structures were determined for ternary complexes of mutant repressors with purines (adenine, guanine, hypoxanthine, and 6-methylpurine) and operator DNA. These structures indicate that R190A binds guanine, hypoxanthine, and adenine with nearly equal, albeit reduced, affinity in large part because of a newly made compensatory hydrogen bond between the rotated hydroxyl side chain of Ser124 and the exocyclic 6 positions of the purines. Through direct and water-mediated contacts, the R190Q protein binds adenine with a nearly 75-fold higher affinity than the wild type repressor while maintaining wild type affinity for guanine and hypoxanthine. The results establish at the atomic level the basis for the critical role of Arg190 in the recognition of the exocyclic 6 position of its purine corepressors and the successful redesign of corepressor specificity.
-
-	Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190.,Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG Biochemistry. 1998 Jan 27;37(4):971-82. PMID:9454587<ref>PMID:9454587</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2pug" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arvidson~~, D N~~]]	+	[[Category: Arvidson DN]]
-	[[Category: Brennan~~, R G~~]]	+	[[Category: Brennan RG]]
-	[[Category: Haldimann, A]]	+	[[Category: Haldimann A]]
-	[[Category: Lu, F]]	+	[[Category: Lu F]]
-	[[Category: Schumacher~~, M A~~]]	+	[[Category: Schumacher MA]]
-	[[Category: Wanner~~, B L~~]]	+	[[Category: Wanner BL]]
-	[[Category: Zalkin, H]]	+	[[Category: Zalkin H]]
-	~~[[Category: Dna-binding regulatory protein]]~~	+
-	~~[[Category: Extended corepressor specificity]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 15:33, 17 June 2021

2021-06-17T15:33:01Z

←Older revision		Revision as of 15:33, 17 June 2021
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	==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==		==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==
-	<StructureSection load='2pug' size='340' side='right' caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2pug' size='340' side='right'caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pug]] is a 2 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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PUG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pug]] is a 2 chain structure with sequence from [https://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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [~~http~~://pdbe.org/2pug PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pug PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pug 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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [https://pdbe.org/2pug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [https://www.ebi.ac.uk/pdbsum/2pug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pug ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PURR_ECOLI PURR_ECOLI]] Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.<ref>PMID:2404765</ref> <ref>PMID:2211500</ref> <ref>PMID:1400170</ref> <ref>PMID:14741201</ref>	+	[[https://www.uniprot.org/uniprot/PURR_ECOLI PURR_ECOLI]] Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.<ref>PMID:2404765</ref> <ref>PMID:2211500</ref> <ref>PMID:1400170</ref> <ref>PMID:14741201</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Arvidson, D N]]		[[Category: Arvidson, D N]]
	[[Category: Brennan, R G]]		[[Category: Brennan, R G]]

OCA at 06:28, 4 April 2018

2018-04-04T06:28:31Z

←Older revision		Revision as of 06:28, 4 April 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==		==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==
	<StructureSection load='2pug' size='340' side='right' caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pug' size='340' side='right' caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [http://pdbe.org/2pug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [http://www.ebi.ac.uk/pdbsum/2pug 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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [http://pdbe.org/2pug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [http://www.ebi.ac.uk/pdbsum/2pug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pug ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pug_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pug_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>
	</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=2pug ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:56, 11 September 2015

2015-09-11T21:56:29Z

←Older revision		Revision as of 21:56, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2pug' size='340' side='right' caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pug' size='340' side='right' caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pug]] is a 2 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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pug]] is a 2 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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [http://www.ebi.ac.uk/pdbsum/2pug 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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [http://pdbe.org/2pug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [http://www.ebi.ac.uk/pdbsum/2pug PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 2pug" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Arvidson, D N]]		[[Category: Arvidson, D N]]
	[[Category: Brennan, R G]]		[[Category: Brennan, R G]]

OCA at 20:06, 25 December 2014

2014-12-25T20:06:54Z

←Older revision		Revision as of 20:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pug]] is a 2 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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pug]] is a 2 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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [http://www.ebi.ac.uk/pdbsum/2pug 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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [http://www.ebi.ac.uk/pdbsum/2pug PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PURR_ECOLI PURR_ECOLI]] Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.<ref>PMID:2404765</ref> <ref>PMID:2211500</ref> <ref>PMID:1400170</ref> <ref>PMID:14741201</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Arvidson, D N.]]	+	[[Category: Arvidson, D N]]
-	[[Category: Brennan, R G.]]	+	[[Category: Brennan, R G]]
-	[[Category: Haldimann, A.]]	+	[[Category: Haldimann, A]]
-	[[Category: Lu, F.]]	+	[[Category: Lu, F]]
-	[[Category: Schumacher, M A.]]	+	[[Category: Schumacher, M A]]
-	[[Category: Wanner, B L.]]	+	[[Category: Wanner, B L]]
-	[[Category: Zalkin, H.]]	+	[[Category: Zalkin, H]]
	[[Category: Dna-binding regulatory protein]]		[[Category: Dna-binding regulatory protein]]
	[[Category: Extended corepressor specificity]]		[[Category: Extended corepressor specificity]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 19:20, 30 September 2014

2014-09-30T19:20:02Z

←Older revision		Revision as of 19:20, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2pug.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==
		+	<StructureSection load='2pug' size='340' side='right' caption='[[2pug]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pug]] is a 2 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=2PUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=2pug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pug OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pug RCSB], [http://www.ebi.ac.uk/pdbsum/2pug 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/pu/2pug_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 ==
		+	Guanine or hypoxanthine, physiological corepressors of the Escherichia coli purine repressor (PurR), promote formation of the ternary PurR-corepressor-operator DNA complex that functions to repress pur operon gene expression. Structure-based predictions on the importance of Arg190 in determining 6-oxopurine specificity and corepressor binding affinity were tested by mutagenesis, analysis of in vivo function, and in vitro corepressor binding measurements. Replacements of Arg190 with Ala or Gln resulted in functional repressors in which binding of guanine and hypoxanthine was retained but specificity was relaxed to permit binding of adenine. X-ray structures were determined for ternary complexes of mutant repressors with purines (adenine, guanine, hypoxanthine, and 6-methylpurine) and operator DNA. These structures indicate that R190A binds guanine, hypoxanthine, and adenine with nearly equal, albeit reduced, affinity in large part because of a newly made compensatory hydrogen bond between the rotated hydroxyl side chain of Ser124 and the exocyclic 6 positions of the purines. Through direct and water-mediated contacts, the R190Q protein binds adenine with a nearly 75-fold higher affinity than the wild type repressor while maintaining wild type affinity for guanine and hypoxanthine. The results establish at the atomic level the basis for the critical role of Arg190 in the recognition of the exocyclic 6 position of its purine corepressors and the successful redesign of corepressor specificity.

-	~~{{STRUCTURE_2pug\| PDB=2pug \| SCENE= }}~~	+	Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190.,Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG Biochemistry. 1998 Jan 27;37(4):971-82. PMID:9454587<ref>PMID:9454587</ref>

-	~~===CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER~~, ~~PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_9454587}}~~	+	==See Also==
-		+	*[[Purine repressor\|Purine repressor]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2pug~~]] is a 2 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=2PUG OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:009454587<~~/~~ref~~><~~ref group="xtra">PMID:015048824</ref><references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Arvidson, D N.]]		[[Category: Arvidson, D N.]]

OCA: Protected "2pug" [edit=sysop:move=sysop]

2013-01-07T11:39:59Z

Protected "2pug" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:39, 7 January 2013

OCA at 11:39, 7 January 2013

2013-01-07T11:39:56Z

←Older revision		Revision as of 11:39, 7 January 2013
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-	{{Seed}}
	[[Image:2pug.png\|left\|200px]]		[[Image:2pug.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pug", 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_2pug\| PDB=2pug \| SCENE= }}		{{STRUCTURE_2pug\| PDB=2pug \| SCENE= }}

	===CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES===		===CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9454587}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9454587 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9454587}}		{{ABSTRACT_PUBMED_9454587}}

	==About this Structure==		==About this Structure==
-	~~2PUG~~ is a 2 ~~chains~~ structure ~~of sequences~~ 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=2PUG OCA].	+	[[2pug]] is a 2 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=2PUG OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9454587~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009454587</ref><ref group="xtra">PMID:015048824</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Arvidson, D N.]]		[[Category: Arvidson, D N.]]
Line 34:		Line 22:
	[[Category: Dna-binding regulatory protein]]		[[Category: Dna-binding regulatory protein]]
	[[Category: Extended corepressor specificity]]		[[Category: Extended corepressor specificity]]
-		+	[[Category: Transcription-dna complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 05:38:44 2009''~~	+

OCA at 03:38, 18 February 2009

2009-02-18T03:38:45Z

←Older revision		Revision as of 03:38, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2PUG 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=2PUG OCA].	+	2PUG is a 2 chains structure of sequences 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=2PUG OCA].

	==Reference==		==Reference==
-	Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190., Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG, Biochemistry. 1998 Jan 27;37(4):971-82. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9454587 9454587]~~	+	<ref group="xtra">PMID:9454587</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Arvidson, D N.]]		[[Category: Arvidson, D N.]]
	[[Category: Brennan, R G.]]		[[Category: Brennan, R G.]]
Line 36:		Line 35:
	[[Category: Extended corepressor specificity]]		[[Category: Extended corepressor specificity]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 12~~:21:~~25 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:38:44 2009''

OCA at 09:21, 29 July 2008

2008-07-29T09:21:30Z

←Older revision		Revision as of 09:21, 29 July 2008
Line 1:		Line 1:
-	[[Image:2pug.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2pug.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2pug\| PDB=2pug \| SCENE= }}		{{STRUCTURE_2pug\| PDB=2pug \| SCENE= }}

-	~~'''~~CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES~~'''~~	+	===CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES===


-	~~==Overview==~~	+	<!--
-	~~Guanine or hypoxanthine~~, ~~physiological corepressors of the Escherichia coli purine repressor (PurR)~~, ~~promote formation of~~ the ~~ternary PurR-corepressor-operator DNA complex that functions~~ to ~~repress pur operon gene expression. Structure-based predictions~~ on ~~the importance of Arg190 in determining 6-oxopurine specificity and corepressor binding affinity were tested by mutagenesis, analysis of in vivo function, and in vitro corepressor binding measurements~~. ~~Replacements of Arg190 with Ala or Gln resulted in functional repressors in which binding of guanine and hypoxanthine was retained but specificity was relaxed to permit binding of adenine~~. ~~X-ray structures were determined for ternary complexes of mutant repressors with purines (adenine, guanine, hypoxanthine, and 6-methylpurine~~) ~~and operator DNA. These structures indicate that R190A binds guanine, hypoxanthine, and adenine with nearly equal, albeit reduced~~, ~~affinity in large part because of a newly made compensatory hydrogen bond between~~ the ~~rotated hydroxyl side chain of Ser124 and the exocyclic 6 positions of the purines~~. ~~Through direct and water~~-~~mediated contacts, the R190Q protein binds adenine with a nearly 75~~-fold higher affinity than the wild type repressor while maintaining wild type affinity for guanine and hypoxanthine. The results establish at the atomic level the basis for the critical role of Arg190 in the recognition of the exocyclic 6 position of its purine corepressors and the successful redesign of corepressor specificity.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9454587}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9454587 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9454587}}

	==About this Structure==		==About this Structure==
Line 31:		Line 35:
	[[Category: Dna-binding regulatory protein]]		[[Category: Dna-binding regulatory protein]]
	[[Category: Extended corepressor specificity]]		[[Category: Extended corepressor specificity]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 13~~:49:24 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 12:21:25 2008''