2h9b - Revision history

OCA at 09:54, 30 August 2023

OCA — Wed, 30 Aug 2023 09:54:11 GMT

←Older revision		Revision as of 09:54, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2h9b' size='340' side='right'caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2h9b' size='340' side='right'caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aciad Aciad~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baylyi_ADP1 Acinetobacter baylyi ADP1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">benM, benR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 ACIAD])~~</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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [https://pdbe.org/2h9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [https://www.ebi.ac.uk/pdbsum/2h9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9b 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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [https://pdbe.org/2h9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [https://www.ebi.ac.uk/pdbsum/2h9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BENM_ACIAD BENM_ACIAD]] Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate.	+	[https://www.uniprot.org/uniprot/BENM_ACIAD BENM_ACIAD] Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciad~~]]	+	[[Category: Acinetobacter baylyi ADP1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Craven~~, S H~~]]	+	[[Category: Craven SH]]
-	[[Category: Ezezika~~, O C~~]]	+	[[Category: Ezezika OC]]
-	[[Category: Momany, C]]	+	[[Category: Momany C]]
-	[[Category: Neidle~~, E L]]~~	+	[[Category: Neidle EL]]
-	~~[[Category: Benm]]~~	+
-	~~[[Category: Lttr]]~~	+
-	~~[[Category: Lysr-type transcriptional regulator]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcriptional activator~~]]	+

OCA at 07:34, 17 March 2021

OCA — Wed, 17 Mar 2021 07:34:30 GMT

←Older revision		Revision as of 07:34, 17 March 2021
Line 1:		Line 1:

	==Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)==		==Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)==
-	<StructureSection load='2h9b' size='340' side='right' caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2h9b' size='340' side='right'caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2H9B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 ACIAD])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 ACIAD])</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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [~~http~~://pdbe.org/2h9b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2h9b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9b 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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [https://pdbe.org/2h9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [https://www.ebi.ac.uk/pdbsum/2h9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BENM_ACIAD BENM_ACIAD]] Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate.	+	[[https://www.uniprot.org/uniprot/BENM_ACIAD BENM_ACIAD]] Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h9/2h9b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h9/2h9b_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2h9b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2h9b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Aciad]]		[[Category: Aciad]]
		+	[[Category: Large Structures]]
	[[Category: Craven, S H]]		[[Category: Craven, S H]]
	[[Category: Ezezika, O C]]		[[Category: Ezezika, O C]]

OCA at 08:08, 18 October 2017

OCA — Wed, 18 Oct 2017 08:08:40 GMT

←Older revision		Revision as of 08:08, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)==		==Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)==
	<StructureSection load='2h9b' size='340' side='right' caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2h9b' size='340' side='right' caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 ACIAD])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 ACIAD])</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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [http://pdbe.org/2h9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [http://www.ebi.ac.uk/pdbsum/2h9b 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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [http://pdbe.org/2h9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [http://www.ebi.ac.uk/pdbsum/2h9b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 05:54, 7 February 2016

OCA — Sun, 07 Feb 2016 05:54:21 GMT

←Older revision		Revision as of 05:54, 7 February 2016
Line 18:		Line 18:
	<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=2h9b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:29, 9 September 2015

OCA — Wed, 09 Sep 2015 22:29:37 GMT

←Older revision		Revision as of 22:29, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='2h9b' size='340' side='right' caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2h9b' size='340' side='right' caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Acinetobacter_sp._adp1 Acinetobacter sp. adp1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 ~~Acinetobacter sp. ADP1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 ACIAD])</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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [http://www.ebi.ac.uk/pdbsum/2h9b 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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [http://pdbe.org/2h9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [http://www.ebi.ac.uk/pdbsum/2h9b PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2h9b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acinetobacter sp. adp1~~]]	+	[[Category: Aciad]]
	[[Category: Craven, S H]]		[[Category: Craven, S H]]
	[[Category: Ezezika, O C]]		[[Category: Ezezika, O C]]

OCA at 08:24, 24 December 2014

OCA — Wed, 24 Dec 2014 08:24:36 GMT

←Older revision		Revision as of 08:24, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._adp1 Acinetobacter sp. adp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9B FirstGlance]. <br>		<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._adp1 Acinetobacter sp. adp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9B FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 Acinetobacter sp. ADP1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 Acinetobacter sp. ADP1])</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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [http://www.ebi.ac.uk/pdbsum/2h9b 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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [http://www.ebi.ac.uk/pdbsum/2h9b PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BENM_ACIAD BENM_ACIAD]] Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Acinetobacter sp. adp1]]		[[Category: Acinetobacter sp. adp1]]
-	[[Category: Craven, S H.]]	+	[[Category: Craven, S H]]
-	[[Category: Ezezika, O C.]]	+	[[Category: Ezezika, O C]]
-	[[Category: Momany, C.]]	+	[[Category: Momany, C]]
-	[[Category: Neidle, E L.]]	+	[[Category: Neidle, E L]]
	[[Category: Benm]]		[[Category: Benm]]
	[[Category: Lttr]]		[[Category: Lttr]]

OCA at 09:08, 30 September 2014

OCA — Tue, 30 Sep 2014 09:08:51 GMT

←Older revision		Revision as of 09:08, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2h9b.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)==
		+	<StructureSection load='2h9b' size='340' side='right' caption='[[2h9b]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._adp1 Acinetobacter sp. adp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2H9B FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6p\|2f6p]], [[2f7a\|2f7a]], [[2f78\|2f78]], [[2f97\|2f97]], [[2f8d\|2f8d]], [[2h98\|2h98]], [[2h99\|2h99]], [[2h9q\|2h9q]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=62977 Acinetobacter sp. ADP1])</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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [http://www.ebi.ac.uk/pdbsum/2h9b 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/h9/2h9b_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 ==
		+	BenM and CatM control transcription of a complex regulon for aromatic compound degradation. These Acinetobacter baylyi paralogues belong to the largest family of prokaryotic transcriptional regulators, the LysR-type proteins. Whereas BenM activates transcription synergistically in response to two effectors, benzoate and cis,cis-muconate, CatM responds only to cis,cis-muconate. Here, site-directed mutagenesis was used to determine the physiological significance of an unexpected benzoate-binding pocket in BenM discovered during structural studies. Residues in BenM were changed to match those of CatM in this hydrophobic pocket. Two BenM residues, R160 and Y293, were found to mediate the response to benzoate. Additionally, alteration of these residues caused benzoate to inhibit activation by cis,cis-muconate, positioned in a separate primary effector-binding site of BenM. The location of the primary site, in an interdomain cleft, is conserved in diverse LysR-type regulators. To improve understanding of this important family, additional regulatory mutants were analysed. The atomic-level structures were characterized of the effector-binding domains of variants that do not require inducers for activation, CatM(R156H) and BenM(R156H,T157S). These structures clearly resemble those of the wild-type proteins in their activated muconate-bound complexes. Amino acid replacements that enable activation without effectors reside at protein interfaces that may impact transcription through effects on oligomerization.

-	~~{{STRUCTURE_2h9b\| PDB=2h9b \| SCENE= }}~~	+	Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.,Craven SH, Ezezika OC, Haddad S, Hall RA, Momany C, Neidle EL Mol Microbiol. 2009 May;72(4):881-94. Epub 2009 Apr 8. PMID:19400783<ref>PMID:19400783</ref>

-	~~===Crystal structure~~ of the ~~effector binding domain of a BenM variant (BenM R156H/T157S)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19400783}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2h9b]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Acinetobacter_sp~~.~~_adp1 Acinetobacter sp. adp1]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019400783<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Acinetobacter sp. adp1]]		[[Category: Acinetobacter sp. adp1]]
	[[Category: Craven, S H.]]		[[Category: Craven, S H.]]

OCA: Protected "2h9b" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 11:25:31 GMT

Protected "2h9b" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:25, 7 January 2013

OCA at 11:25, 7 January 2013

OCA — Mon, 07 Jan 2013 11:25:26 GMT

←Older revision		Revision as of 11:25, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2h9b.png\|left\|200px]]		[[Image:2h9b.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2h9b", 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_2h9b\| PDB=2h9b \| SCENE= }}		{{STRUCTURE_2h9b\| PDB=2h9b \| SCENE= }}

	===Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)===		===Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19400783}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19400783 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19400783}}		{{ABSTRACT_PUBMED_19400783}}

	==About this Structure==		==About this Structure==
-	~~2H9B~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Acinetobacter_sp._adp1 Acinetobacter sp. adp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA].	+	[[2h9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._adp1 Acinetobacter sp. adp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19400783~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019400783</ref><references group="xtra"/>
	[[Category: Acinetobacter sp. adp1]]		[[Category: Acinetobacter sp. adp1]]
	[[Category: Craven, S H.]]		[[Category: Craven, S H.]]
Line 32:		Line 20:
	[[Category: Lttr]]		[[Category: Lttr]]
	[[Category: Lysr-type transcriptional regulator]]		[[Category: Lysr-type transcriptional regulator]]
		+	[[Category: Transcription]]
	[[Category: Transcriptional activator]]		[[Category: Transcriptional activator]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 16:05:35 2009''

OCA at 13:05, 20 May 2009

OCA — Wed, 20 May 2009 13:05:37 GMT

←Older revision		Revision as of 13:05, 20 May 2009
Line 12:		Line 12:
	===Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)===		===Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19400783}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19400783 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19400783}}

	==About this Structure==		==About this Structure==
-	2H9B is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA].	+	2H9B is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_sp._adp1 Acinetobacter sp. adp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA].
-	[[Category: Acinetobacter sp.]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:19400783</ref><references group="xtra"/>
		+	[[Category: Acinetobacter sp. adp1]]
	[[Category: Craven, S H.]]		[[Category: Craven, S H.]]
	[[Category: Ezezika, O C.]]		[[Category: Ezezika, O C.]]
Line 25:		Line 34:
	[[Category: Transcriptional activator]]		[[Category: Transcriptional activator]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Feb~~ 16 11:46:55 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 16:05:35 2009''