1qqi - Revision history

OCA at 09:02, 22 May 2024

OCA — Wed, 22 May 2024 09:02:16 GMT

←Older revision		Revision as of 09:02, 22 May 2024
Line 19:		Line 19:
	</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=1qqi 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=1qqi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PhoB is a transcriptional activator that binds to the phosphate box in the promoters of the phosphate genes of Escherichia coli. PhoB contains two functional domains, an N-terminal phosphorylation domain and a C-terminal DNA-binding/transactivation domain. Here, the three-dimensional structure of the DNA-binding/transactivation domain has been determined by NMR. It consists of an N-terminal four-stranded beta-sheet, a central three helical bundle and a C-terminal beta-hairpin. The second and third helices form a helix-turn-helix (HTH) variant containing a longer turn than the corresponding turn of the classical HTH motif. The overall architecture is very close to that of the OmpR DNA-binding/transactivation domain, however, the conformation of the long turn region of PhoB, a putative interaction site for the RNA polymerase sigma subunit, is entirely different from that of the corresponding turn of OmpR, which interacts with the alpha subunit. In addition, the third helix of PhoB is three amino acid residues longer than the corresponding helix of OmpR. The binding site of PhoB is a TGTCA sequence and the phospahte box contains the two binding sites. NMR studies of the complexes of the PhoB DNA-binding/transactivation domain bound to several different DNA molecules have revealed that two PhoB molecules bind in a tandem array on the phosphate box. In each complex of PhoB the third helix of the DNA-binding/transactivation domain is likely to recognize the TGTCA sequence from the major groove of DNA and the C-terminal beta-hairpin contacts on the minor groove of the 3' site out of the TGTCA sequence in a non-specific manner. The long turn region facing outward is likely to interact with the sigma subunit.
		+
		+	Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box.,Okamura H, Hanaoka S, Nagadoi A, Makino K, Nishimura Y J Mol Biol. 2000 Feb 4;295(5):1225-36. PMID:10653699<ref>PMID:10653699</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1qqi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:06, 17 April 2024

OCA — Wed, 17 Apr 2024 06:06:27 GMT

←Older revision		Revision as of 06:06, 17 April 2024
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI==		==SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI==
-	<StructureSection load='1qqi' size='340' side='right'caption='[[1qqi~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1qqi' size='340' side='right'caption='[[1qqi]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QQI FirstGlance]. <br>
-	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [https://pdbe.org/1qqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [https://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qqi ProSAT], [https://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [https://pdbe.org/1qqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [https://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qqi ProSAT], [https://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PHOB_ECOLI PHOB_ECOLI]] This protein is a positive regulator for the phosphate regulon. Transcription of this operon is positively regulated by PhoB and PhoR when phosphate is limited.	+	[https://www.uniprot.org/uniprot/PHOB_ECOLI PHOB_ECOLI] This protein is a positive regulator for the phosphate regulon. Transcription of this operon is positively regulated by PhoB and PhoR when phosphate is limited.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</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=1qqi 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=1qqi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	PhoB is a transcriptional activator that binds to the phosphate box in the promoters of the phosphate genes of Escherichia coli. PhoB contains two functional domains, an N-terminal phosphorylation domain and a C-terminal DNA-binding/transactivation domain. Here, the three-dimensional structure of the DNA-binding/transactivation domain has been determined by NMR. It consists of an N-terminal four-stranded beta-sheet, a central three helical bundle and a C-terminal beta-hairpin. The second and third helices form a helix-turn-helix (HTH) variant containing a longer turn than the corresponding turn of the classical HTH motif. The overall architecture is very close to that of the OmpR DNA-binding/transactivation domain, however, the conformation of the long turn region of PhoB, a putative interaction site for the RNA polymerase sigma subunit, is entirely different from that of the corresponding turn of OmpR, which interacts with the alpha subunit. In addition, the third helix of PhoB is three amino acid residues longer than the corresponding helix of OmpR. The binding site of PhoB is a TGTCA sequence and the phospahte box contains the two binding sites. NMR studies of the complexes of the PhoB DNA-binding/transactivation domain bound to several different DNA molecules have revealed that two PhoB molecules bind in a tandem array on the phosphate box. In each complex of PhoB the third helix of the DNA-binding/transactivation domain is likely to recognize the TGTCA sequence from the major groove of DNA and the C-terminal beta-hairpin contacts on the minor groove of the 3' site out of the TGTCA sequence in a non-specific manner. The long turn region facing outward is likely to interact with the sigma subunit.
-
-	Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box.,Okamura H, Hanaoka S, Nagadoi A, Makino K, Nishimura Y J Mol Biol. 2000 Feb 4;295(5):1225-36. PMID:10653699<ref>PMID:10653699</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qqi" 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: Hanaoka, S]]	+	[[Category: Hanaoka S]]
-	[[Category: Makino, K]]	+	[[Category: Makino K]]
-	[[Category: Nagadoi, A]]	+	[[Category: Nagadoi A]]
-	[[Category: Nishimura, Y]]	+	[[Category: Nishimura Y]]
-	[[Category: Okamura, H]]	+	[[Category: Okamura H]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Winged helix-turn-helix~~]]	+

OCA at 10:01, 15 September 2021

OCA — Wed, 15 Sep 2021 10:01:28 GMT

←Older revision		Revision as of 10:01, 15 September 2021
Line 3:		Line 3:
	<StructureSection load='1qqi' size='340' side='right'caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1qqi' size='340' side='right'caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QQI FirstGlance]. <br>
-	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [~~http~~://pdbe.org/1qqi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qqi ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>	+	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [https://pdbe.org/1qqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [https://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qqi ProSAT], [https://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PHOB_ECOLI PHOB_ECOLI]] This protein is a positive regulator for the phosphate regulon. Transcription of this operon is positively regulated by PhoB and PhoR when phosphate is limited.	+	[[https://www.uniprot.org/uniprot/PHOB_ECOLI PHOB_ECOLI]] This protein is a positive regulator for the phosphate regulon. Transcription of this operon is positively regulated by PhoB and PhoR when phosphate is limited.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:16, 4 December 2019

OCA — Wed, 04 Dec 2019 11:16:27 GMT

←Older revision		Revision as of 11:16, 4 December 2019
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI==		==SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI==
-	<StructureSection load='1qqi' size='340' side='right' caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1qqi' size='340' side='right'caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Hanaoka, S]]		[[Category: Hanaoka, S]]
	[[Category: Makino, K]]		[[Category: Makino, K]]

OCA at 07:41, 28 February 2018

OCA — Wed, 28 Feb 2018 07:41:44 GMT

←Older revision		Revision as of 07:41, 28 February 2018
Line 1:		Line 1:
		+
	==SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI==		==SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI==
	<StructureSection load='1qqi' size='340' side='right' caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1qqi' size='340' side='right' caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>
-	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [http://pdbe.org/1qqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [http://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [http://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>	+	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [http://pdbe.org/1qqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [http://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qqi ProSAT], [http://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/1qqi_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/1qqi_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>

OCA at 22:26, 7 February 2016

OCA — Sun, 07 Feb 2016 22:26:56 GMT

←Older revision		Revision as of 22:26, 7 February 2016
Line 15:		Line 15:
	<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=1qqi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:27, 10 September 2015

OCA — Thu, 10 Sep 2015 05:27:50 GMT

←Older revision		Revision as of 05:27, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1qqi' size='340' side='right' caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1qqi' size='340' side='right' caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>
-	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [http://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [http://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>	+	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [http://pdbe.org/1qqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [http://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [http://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	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 1qqi" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Hanaoka, S]]		[[Category: Hanaoka, S]]
	[[Category: Makino, K]]		[[Category: Makino, K]]

OCA at 18:36, 24 December 2014

OCA — Wed, 24 Dec 2014 18:36:12 GMT

←Older revision		Revision as of 18:36, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>
-	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [http://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [http://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>	+	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [http://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [http://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PHOB_ECOLI PHOB_ECOLI]] This protein is a positive regulator for the phosphate regulon. Transcription of this operon is positively regulated by PhoB and PhoR when phosphate is limited.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Hanaoka, S.]]	+	[[Category: Hanaoka, S]]
-	[[Category: Makino, K.]]	+	[[Category: Makino, K]]
-	[[Category: Nagadoi, A.]]	+	[[Category: Nagadoi, A]]
-	[[Category: Nishimura, Y.]]	+	[[Category: Nishimura, Y]]
-	[[Category: Okamura, H~~.]]~~	+	[[Category: Okamura, H]]
-	~~[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]~~	+
-	~~[[Category: Riken structural genomics/proteomics initiative]]~~	+
-	~~[[Category: Rsgi~~]]	+
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
		+	[[Category: Rsgi]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Winged helix-turn-helix]]		[[Category: Winged helix-turn-helix]]

OCA at 14:58, 29 September 2014

OCA — Mon, 29 Sep 2014 14:58:17 GMT

←Older revision		Revision as of 14:58, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1qqi.~~png\|left~~\|200px]]	+	==SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI==
		+	<StructureSection load='1qqi' size='340' side='right' caption='[[1qqi]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQI FirstGlance]. <br>
		+	</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=1qqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qqi RCSB], [http://www.ebi.ac.uk/pdbsum/1qqi PDBsum], [http://www.topsan.org/Proteins/RSGI/1qqi TOPSAN]</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/qq/1qqi_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 ==
		+	PhoB is a transcriptional activator that binds to the phosphate box in the promoters of the phosphate genes of Escherichia coli. PhoB contains two functional domains, an N-terminal phosphorylation domain and a C-terminal DNA-binding/transactivation domain. Here, the three-dimensional structure of the DNA-binding/transactivation domain has been determined by NMR. It consists of an N-terminal four-stranded beta-sheet, a central three helical bundle and a C-terminal beta-hairpin. The second and third helices form a helix-turn-helix (HTH) variant containing a longer turn than the corresponding turn of the classical HTH motif. The overall architecture is very close to that of the OmpR DNA-binding/transactivation domain, however, the conformation of the long turn region of PhoB, a putative interaction site for the RNA polymerase sigma subunit, is entirely different from that of the corresponding turn of OmpR, which interacts with the alpha subunit. In addition, the third helix of PhoB is three amino acid residues longer than the corresponding helix of OmpR. The binding site of PhoB is a TGTCA sequence and the phospahte box contains the two binding sites. NMR studies of the complexes of the PhoB DNA-binding/transactivation domain bound to several different DNA molecules have revealed that two PhoB molecules bind in a tandem array on the phosphate box. In each complex of PhoB the third helix of the DNA-binding/transactivation domain is likely to recognize the TGTCA sequence from the major groove of DNA and the C-terminal beta-hairpin contacts on the minor groove of the 3' site out of the TGTCA sequence in a non-specific manner. The long turn region facing outward is likely to interact with the sigma subunit.

-	~~{{STRUCTURE_1qqi\| PDB=1qqi \| SCENE= }}~~	+	Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box.,Okamura H, Hanaoka S, Nagadoi A, Makino K, Nishimura Y J Mol Biol. 2000 Feb 4;295(5):1225-36. PMID:10653699<ref>PMID:10653699</ref>

-	~~===SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10653699}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1qqi]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1QQI OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010653699<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Hanaoka, S.]]		[[Category: Hanaoka, S.]]

OCA: Protected "1qqi" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 09:54:55 GMT

Protected "1qqi" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:54, 2 January 2013