2pub - Revision history

OCA at 09:12, 21 February 2024

2024-02-21T09:12:01Z

← Older revision		Revision as of 09:12, 21 February 2024
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	<StructureSection load='2pub' size='340' side='right'caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pub' size='340' side='right'caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pub]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUB FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADE:ADENINE'>ADE</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=ADE:ADENINE'>ADE</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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [https://pdbe.org/2pub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [https://www.ebi.ac.uk/pdbsum/2pub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pub 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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [https://pdbe.org/2pub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [https://www.ebi.ac.uk/pdbsum/2pub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pub 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]]
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	</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=2pub 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=2pub ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.

	Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices.,Schumacher MA, Choi KY, Zalkin H, Brennan RG Science. 1994 Nov 4;266(5186):763-70. PMID:7973627<ref>PMID:7973627</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2pub" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Brennan, M A~~]]		[[Category: Synthetic construct]]
	[[Category: ~~Choi, K Y~~]]		[[Category: Brennan MA]]
	[[Category: ~~Schumacher, R G~~]]		[[Category: Choi KY]]
	[[Category: ~~Zalkin, H~~]]		[[Category: Schumacher RG]]
	[[Category: ~~Dna-binding regulatory protein]]~~		[[Category: Zalkin H]]
	~~[[Category: Transcription-dna complex~~]]

OCA at 15:32, 17 June 2021

2021-06-17T15:32:55Z

← Older revision		Revision as of 15:32, 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='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pub' size='340' side='right'caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [~~http~~://pdbe.org/2pub PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pub PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pub 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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [https://pdbe.org/2pub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [https://www.ebi.ac.uk/pdbsum/2pub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pub 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: Brennan, M A]]		[[Category: Brennan, M A]]
	[[Category: Choi, K Y]]		[[Category: Choi, K Y]]

OCA at 06:28, 4 April 2018

2018-04-04T06:28:21Z

← Older revision		Revision as of 06:28, 4 April 2018
Line 3:		Line 3:
	<StructureSection load='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pub]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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='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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://pdbe.org/2pub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pub 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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://pdbe.org/2pub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pub ProSAT]</span></td></tr>
	</table>		</table>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pub_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pub_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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacillus coli migula 1895]]
	[[Category: Brennan, M A]]		[[Category: Brennan, M A]]
	[[Category: Choi, K Y]]		[[Category: Choi, K Y]]

OCA at 06:54, 9 March 2017

2017-03-09T06:54:23Z

← Older revision		Revision as of 06:54, 9 March 2017
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='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pub]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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='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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://pdbe.org/2pub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pub 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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://pdbe.org/2pub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus coli migula 1895~~]]		[[Category: Brennan, M A]]
	[[Category: Choi, K Y]]		[[Category: Choi, K Y]]
	[[Category: Schumacher, R G~~.Brennan M A~~]]		[[Category: Schumacher, R G]]
	[[Category: Zalkin, H]]		[[Category: Zalkin, H]]
	[[Category: Dna-binding regulatory protein]]		[[Category: Dna-binding regulatory protein]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 09:01, 8 February 2016

2016-02-08T09:01:55Z

← Older revision		Revision as of 09:01, 8 February 2016
Line 17:		Line 17:
	<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=2pub ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:59, 10 September 2015

2015-09-10T09:59:50Z

← Older revision		Revision as of 09:59, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub 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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://pdbe.org/2pub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub 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 2pub" 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: Choi, K Y]]		[[Category: Choi, K Y]]
	[[Category: Schumacher, R G.Brennan M A]]		[[Category: Schumacher, R G.Brennan M A]]

OCA at 22:08, 24 December 2014

2014-12-24T22:08:39Z

← Older revision		Revision as of 22:08, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub 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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub 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]]
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	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Choi, K Y.]]		[[Category: Choi, K Y]]
	[[Category: Schumacher, R G.Brennan M A.]]		[[Category: Schumacher, R G.Brennan M A]]
	[[Category: Zalkin, H.]]		[[Category: Zalkin, H]]
	[[Category: Dna-binding regulatory protein]]		[[Category: Dna-binding regulatory protein]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 18:02, 30 September 2014

2014-09-30T18:02:24Z

← Older revision		Revision as of 18:02, 30 September 2014
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	[[Image:~~2pub~~.~~png~~\|~~left~~\|~~200px~~]]		==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==
			<StructureSection load='2pub' size='340' side='right' caption='[[2pub]], [[Resolution\|resolution]] 2.70Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2pub]] 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=2PUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUB FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=2pub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pub RCSB], [http://www.ebi.ac.uk/pdbsum/2pub 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/2pub_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 ==
			The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.

	~~{{STRUCTURE_2pub\| PDB=2pub \| SCENE= }}~~		Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices.,Schumacher MA, Choi KY, Zalkin H, Brennan RG Science. 1994 Nov 4;266(5186):763-70. PMID:7973627<ref>PMID:7973627</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_7973627}}~~		==See Also==
			*[[Purine repressor\|Purine repressor]]
	==~~About this Structure~~==		== References ==
	[[~~2pub]] 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=2PUB OCA~~].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:007973627<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Choi, K Y.]]		[[Category: Choi, K Y.]]

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

2013-01-07T10:18:50Z

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

← Older revision	Revision as of 10:18, 7 January 2013
(No difference)

OCA at 10:18, 7 January 2013

2013-01-07T10:18:48Z

← Older revision		Revision as of 10:18, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2pub.png\|left\|200px]]		[[Image:2pub.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2pub", 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_2pub\| PDB=2pub \| SCENE= }}		{{STRUCTURE_2pub\| PDB=2pub \| 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_7973627}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 7973627 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_7973627}}		{{ABSTRACT_PUBMED_7973627}}

	==About this Structure==		==About this Structure==
	~~2PUB~~ 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=2PUB OCA].		[[2pub]] 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=2PUB OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~7973627~~</ref><references group="xtra"/>		<ref group="xtra">PMID:007973627</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Choi, K Y.]]		[[Category: Choi, K Y.]]
Line 29:		Line 17:
	[[Category: Zalkin, H.]]		[[Category: Zalkin, H.]]
	[[Category: Dna-binding regulatory protein]]		[[Category: Dna-binding regulatory protein]]
			[[Category: Transcription-dna complex]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 20:48:49 2009''~~