2ca9 - Revision history

OCA at 07:48, 23 October 2024

2024-10-23T07:48:45Z

← Older revision		Revision as of 07:48, 23 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/2ca9_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/2ca9_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2ca9 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=2ca9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The survival of Helicobacter pylori in the human stomach critically relies on the availability and use of nickel, an absolute cofactor of the important virulence determinant urease. Nickel-responsive gene regulation is mediated by HpNikR, a protein belonging to the ribbon-helix-helix family of transcriptional regulators. Unlike its homologues, HpNikR acts as both a repressor and an activator within an acid adaptation cascade. We report the crystal structure of the full-length HpNikR in a nickel-free conformation and two nickel-bound structures obtained in different conditions: Ni1-HpNikR and Ni2-HpNikR. Apo-HpNikR shows the same global fold as its bacterial homologues although with an unusual closed trans-conformation and asymmetrical quaternary arrangement. The structure of Ni1-HpNikR in the presence of nickel has two different sides, one showing nickel binding similar to that of known NikRs and the other reflecting an intermediate state. The structure of Ni2-HpNikR obtained using a shorter exposure to nickel provides another snapshot of the nickel incorporation. Altogether, the three structures have allowed us to determine the route for nickel within HpNikR and reveal the cooperativity between the tetramerization domain and the DNA-binding domain. Experiments using point mutations of HpnikR residues involved in nickel internalisation confirm that these residues are critical for HpNikR functions in vivo.

			Structural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel-bound states.,Dian C, Schauer K, Kapp U, McSweeney SM, Labigne A, Terradot L J Mol Biol. 2006 Aug 25;361(4):715-30. Epub 2006 Jul 7. PMID:16872629<ref>PMID:16872629</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 2ca9" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:38, 1 May 2024

2024-05-01T06:38:42Z

← Older revision		Revision as of 06:38, 1 May 2024
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	<StructureSection load='2ca9' size='340' side='right'caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2ca9' size='340' side='right'caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.05Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height~~: ~~3em;~~'>~~[[2cad\|2cad]], [[2caj\|2caj]]~~</~~div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [https://pdbe.org/2ca9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ca9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ca9 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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [https://pdbe.org/2ca9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ca9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ca9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY]] Transcriptional regulator (Potential).		[https://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY] Transcriptional regulator (Potential).
	== 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=2ca9 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=2ca9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The survival of Helicobacter pylori in the human stomach critically relies on the availability and use of nickel, an absolute cofactor of the important virulence determinant urease. Nickel-responsive gene regulation is mediated by HpNikR, a protein belonging to the ribbon-helix-helix family of transcriptional regulators. Unlike its homologues, HpNikR acts as both a repressor and an activator within an acid adaptation cascade. We report the crystal structure of the full-length HpNikR in a nickel-free conformation and two nickel-bound structures obtained in different conditions: Ni1-HpNikR and Ni2-HpNikR. Apo-HpNikR shows the same global fold as its bacterial homologues although with an unusual closed trans-conformation and asymmetrical quaternary arrangement. The structure of Ni1-HpNikR in the presence of nickel has two different sides, one showing nickel binding similar to that of known NikRs and the other reflecting an intermediate state. The structure of Ni2-HpNikR obtained using a shorter exposure to nickel provides another snapshot of the nickel incorporation. Altogether, the three structures have allowed us to determine the route for nickel within HpNikR and reveal the cooperativity between the tetramerization domain and the DNA-binding domain. Experiments using point mutations of HpnikR residues involved in nickel internalisation confirm that these residues are critical for HpNikR functions in vivo.

	Structural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel-bound states.,Dian C, Schauer K, Kapp U, McSweeney SM, Labigne A, Terradot L J Mol Biol. 2006 Aug 25;361(4):715-30. Epub 2006 Jul 7. PMID:16872629<ref>PMID:16872629</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2ca9" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Campylobacter~~ pylori]]		[[Category: Helicobacter pylori 26695]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Dian, C]]		[[Category: Dian C]]
	[[Category: Kapp, U]]		[[Category: Kapp U]]
	[[Category: Labigne, A]]		[[Category: Labigne A]]
	[[Category: McSweeney~~, S M~~]]		[[Category: McSweeney SM]]
	[[Category: Schauer, K]]		[[Category: Schauer K]]
	[[Category: Terradot, L]]		[[Category: Terradot L]]
	~~[[Category: Acidic-adaptive response]]~~
	~~[[Category: Dna-binding]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Nickel uptake]]~~
	~~[[Category: Ribbon-helix-helix]]~~
	~~[[Category: Transcription]]~~
	~~[[Category: Transcription regulator]]~~
	~~[[Category: Transcriptional regulation~~]]

OCA at 06:51, 1 December 2021

2021-12-01T06:51:42Z

← Older revision		Revision as of 06:51, 1 December 2021
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	<StructureSection load='2ca9' size='340' side='right'caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2ca9' size='340' side='right'caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2cad\|2cad]], [[2caj\|2caj]]</div></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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [~~http~~://pdbe.org/2ca9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ca9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ca9 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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [https://pdbe.org/2ca9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ca9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ca9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY]] Transcriptional regulator (Potential).		[[https://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY]] Transcriptional regulator (Potential).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:00, 26 February 2020

2020-02-26T11:00:50Z

← Older revision		Revision as of 11:00, 26 February 2020
Line 1:		Line 1:

	==apo-NIKR from helicobacter pylori in closed trans-conformation==		==apo-NIKR from helicobacter pylori in closed trans-conformation==
	<StructureSection load='2ca9' size='340' side='right' caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2ca9' size='340' side='right'caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Campylobacter pylori]]		[[Category: Campylobacter pylori]]
			[[Category: Large Structures]]
	[[Category: Dian, C]]		[[Category: Dian, C]]
	[[Category: Kapp, U]]		[[Category: Kapp, U]]

OCA at 08:25, 23 May 2018

2018-05-23T08:25:40Z

← Older revision		Revision as of 08:25, 23 May 2018
Line 1:		Line 1:

	==apo-NIKR from helicobacter pylori in closed trans-conformation==		==apo-NIKR from helicobacter pylori in closed trans-conformation==
	<StructureSection load='2ca9' size='340' side='right' caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2ca9' size='340' side='right' caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [http://pdbe.org/2ca9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ca9 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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [http://pdbe.org/2ca9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ca9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ca9 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/ca/2ca9_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/2ca9_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 23:57, 9 February 2016

2016-02-09T23:57:26Z

← Older revision		Revision as of 23:57, 9 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=2ca9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:19, 11 September 2015

2015-09-11T03:19:59Z

← Older revision		Revision as of 03:19, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2ca9' size='340' side='right' caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2ca9' size='340' side='right' caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Helicobacter_pylori_26695 Helicobacter~~ pylori ~~26695~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ca9 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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [http://pdbe.org/2ca9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ca9 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 2ca9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Helicobacter~~ pylori ~~26695~~]]		[[Category: Campylobacter pylori]]
	[[Category: Dian, C]]		[[Category: Dian, C]]
	[[Category: Kapp, U]]		[[Category: Kapp, U]]

OCA at 10:24, 25 December 2014

2014-12-25T10:24:19Z

← Older revision		Revision as of 10:24, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ca9 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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ca9 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY]] Transcriptional regulator (Potential).
	== 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: Helicobacter pylori 26695]]		[[Category: Helicobacter pylori 26695]]
	[[Category: Dian, C.]]		[[Category: Dian, C]]
	[[Category: Kapp, U.]]		[[Category: Kapp, U]]
	[[Category: Labigne, A.]]		[[Category: Labigne, A]]
	[[Category: McSweeney, S M.]]		[[Category: McSweeney, S M]]
	[[Category: Schauer, K.]]		[[Category: Schauer, K]]
	[[Category: Terradot, L.]]		[[Category: Terradot, L]]
	[[Category: Acidic-adaptive response]]		[[Category: Acidic-adaptive response]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 01:56, 30 September 2014

2014-09-30T01:56:18Z

← Older revision		Revision as of 01:56, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2ca9~~.~~png~~\|~~left~~\|~~200px~~]]		==apo-NIKR from helicobacter pylori in closed trans-conformation==
			<StructureSection load='2ca9' size='340' side='right' caption='[[2ca9]], [[Resolution\|resolution]] 2.05Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CA9 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cad\|2cad]], [[2caj\|2caj]]</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=2ca9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ca9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ca9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ca9 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/ca/2ca9_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 survival of Helicobacter pylori in the human stomach critically relies on the availability and use of nickel, an absolute cofactor of the important virulence determinant urease. Nickel-responsive gene regulation is mediated by HpNikR, a protein belonging to the ribbon-helix-helix family of transcriptional regulators. Unlike its homologues, HpNikR acts as both a repressor and an activator within an acid adaptation cascade. We report the crystal structure of the full-length HpNikR in a nickel-free conformation and two nickel-bound structures obtained in different conditions: Ni1-HpNikR and Ni2-HpNikR. Apo-HpNikR shows the same global fold as its bacterial homologues although with an unusual closed trans-conformation and asymmetrical quaternary arrangement. The structure of Ni1-HpNikR in the presence of nickel has two different sides, one showing nickel binding similar to that of known NikRs and the other reflecting an intermediate state. The structure of Ni2-HpNikR obtained using a shorter exposure to nickel provides another snapshot of the nickel incorporation. Altogether, the three structures have allowed us to determine the route for nickel within HpNikR and reveal the cooperativity between the tetramerization domain and the DNA-binding domain. Experiments using point mutations of HpnikR residues involved in nickel internalisation confirm that these residues are critical for HpNikR functions in vivo.

	~~{{STRUCTURE_2ca9\| PDB=2ca9 \| SCENE= }}~~		Structural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel-bound states.,Dian C, Schauer K, Kapp U, McSweeney SM, Labigne A, Terradot L J Mol Biol. 2006 Aug 25;361(4):715-30. Epub 2006 Jul 7. PMID:16872629<ref>PMID:16872629</ref>

	~~===apo-NIKR from helicobacter pylori in closed trans-conformation===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16872629}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2ca9]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016872629<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Helicobacter pylori 26695]]		[[Category: Helicobacter pylori 26695]]
	[[Category: Dian, C.]]		[[Category: Dian, C.]]

OCA at 12:34, 6 March 2013

2013-03-06T12:34:24Z

← Older revision		Revision as of 12:34, 6 March 2013
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	{{STRUCTURE_2ca9\| PDB=2ca9 \| SCENE= }}		{{STRUCTURE_2ca9\| PDB=2ca9 \| SCENE= }}

	===~~APO~~-NIKR ~~FROM HELICOBACTER PYLORI IN CLOSED TRANS~~-~~CONFORMATION~~===		===apo-NIKR from helicobacter pylori in closed trans-conformation===

	{{ABSTRACT_PUBMED_16872629}}		{{ABSTRACT_PUBMED_16872629}}

	==About this Structure==		==About this Structure==
	[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Helicobacter_pylori~~ Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA].		[[2ca9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CA9 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:016872629</ref><references group="xtra"/>		<ref group="xtra">PMID:016872629</ref><references group="xtra"/>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori 26695]]
	[[Category: Dian, C.]]		[[Category: Dian, C.]]
	[[Category: Kapp, U.]]		[[Category: Kapp, U.]]
	[[Category: Labigne, A.]]		[[Category: Labigne, A.]]
	[[Category: ~~Mcsweeney~~, S M.]]		[[Category: McSweeney, S M.]]
	[[Category: Schauer, K.]]		[[Category: Schauer, K.]]
	[[Category: Terradot, L.]]		[[Category: Terradot, L.]]
	[[Category: Acidic-adaptive response]]		[[Category: Acidic-adaptive response]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	~~[[Category: Hypothetical protein]]~~
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	~~[[Category: Nickel]]~~
	[[Category: Nickel uptake]]		[[Category: Nickel uptake]]
	[[Category: Ribbon-helix-helix]]		[[Category: Ribbon-helix-helix]]
			[[Category: Transcription]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]
	[[Category: Transcriptional regulation]]		[[Category: Transcriptional regulation]]