2f8d - Revision history

OCA at 09:22, 30 August 2023

2023-08-30T09:22:30Z

← Older revision		Revision as of 09:22, 30 August 2023
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	<StructureSection load='2f8d' size='340' side='right'caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2f8d' size='340' side='right'caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Acibi Acibi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F8D FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.7Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]~~</~~div~~><~~/td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">benM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])~~</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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [https://pdbe.org/2f8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [https://www.ebi.ac.uk/pdbsum/2f8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8d 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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [https://pdbe.org/2f8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [https://www.ebi.ac.uk/pdbsum/2f8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8d 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: ~~Acibi~~]]		[[Category: Acinetobacter baylyi]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ezezika~~, O C~~]]		[[Category: Ezezika OC]]
	[[Category: Haddad, S]]		[[Category: Haddad S]]
	[[Category: Momany, C]]		[[Category: Momany C]]
	[[Category: Neidle~~, E L]]~~		[[Category: Neidle EL]]
	~~[[Category: Benm]]~~
	~~[[Category: Effector binding domain]]~~
	~~[[Category: Gene regulation]]~~
	~~[[Category: Inducer binding domain]]~~
	~~[[Category: Lttr]]~~
	~~[[Category: Lysr-type transcriptional regulator]]~~
	~~[[Category: Tetramerization~~]]

OCA at 07:13, 24 February 2021

2021-02-24T07:13:13Z

← Older revision		Revision as of 07:13, 24 February 2021
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	==BenM effector-Binding domain crystallized from high pH conditions==		==BenM effector-Binding domain crystallized from high pH conditions==
	<StructureSection load='2f8d' size='340' side='right' caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2f8d' size='340' side='right'caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Acibi Acibi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2F8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acibi Acibi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F8D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])</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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [~~http~~://pdbe.org/2f8d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2f8d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8d 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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [https://pdbe.org/2f8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [https://www.ebi.ac.uk/pdbsum/2f8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8d 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/f8/2f8d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f8/2f8d_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</StructureSection>		</StructureSection>
	[[Category: Acibi]]		[[Category: Acibi]]
			[[Category: Large Structures]]
	[[Category: Ezezika, O C]]		[[Category: Ezezika, O C]]
	[[Category: Haddad, S]]		[[Category: Haddad, S]]

OCA at 07:35, 18 October 2017

2017-10-18T07:35:05Z

← Older revision		Revision as of 07:35, 18 October 2017
Line 1:		Line 1:

	==BenM effector-Binding domain crystallized from high pH conditions==		==BenM effector-Binding domain crystallized from high pH conditions==
	<StructureSection load='2f8d' size='340' side='right' caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2f8d' size='340' side='right' caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])</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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [http://pdbe.org/2f8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [http://www.ebi.ac.uk/pdbsum/2f8d 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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [http://pdbe.org/2f8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [http://www.ebi.ac.uk/pdbsum/2f8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=2f8d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:34, 11 September 2015

2015-09-11T23:34:40Z

← Older revision		Revision as of 23:34, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2f8d' size='340' side='right' caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2f8d' size='340' side='right' caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Acinetobacter_baylyi Acinetobacter baylyi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acibi Acibi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F8D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ~~Acinetobacter baylyi~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])</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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [http://www.ebi.ac.uk/pdbsum/2f8d 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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [http://pdbe.org/2f8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [http://www.ebi.ac.uk/pdbsum/2f8d PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2f8d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Acinetobacter baylyi~~]]		[[Category: Acibi]]
	[[Category: Ezezika, O C]]		[[Category: Ezezika, O C]]
	[[Category: Haddad, S]]		[[Category: Haddad, S]]

OCA at 20:53, 25 December 2014

2014-12-25T20:53:58Z

← Older revision		Revision as of 20:53, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F8D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 Acinetobacter baylyi])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 Acinetobacter baylyi])</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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [http://www.ebi.ac.uk/pdbsum/2f8d 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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [http://www.ebi.ac.uk/pdbsum/2f8d 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 baylyi]]		[[Category: Acinetobacter baylyi]]
	[[Category: Ezezika, O C.]]		[[Category: Ezezika, O C]]
	[[Category: Haddad, S.]]		[[Category: Haddad, S]]
	[[Category: Momany, C.]]		[[Category: Momany, C]]
	[[Category: Neidle, E L.]]		[[Category: Neidle, E L]]
	[[Category: Benm]]		[[Category: Benm]]
	[[Category: Effector binding domain]]		[[Category: Effector binding domain]]

OCA at 23:45, 29 September 2014

2014-09-29T23:45:43Z

← Older revision		Revision as of 23:45, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2f8d~~.~~png~~\|~~left~~\|~~200px~~]]		==BenM effector-Binding domain crystallized from high pH conditions==
			<StructureSection load='2f8d' size='340' side='right' caption='[[2f8d]], [[Resolution\|resolution]] 2.70Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2f8d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F8D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f6g\|2f6g]], [[2f6p\|2f6p]], [[2f78\|2f78]], [[2f7a\|2f7a]], [[2f7b\|2f7b]], [[2f7c\|2f7c]], [[2f97\|2f97]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">benM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 Acinetobacter baylyi])</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=2f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f8d RCSB], [http://www.ebi.ac.uk/pdbsum/2f8d 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/f8/2f8d_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 ==
			LysR-type transcriptional regulators comprise the largest family of homologous regulatory DNA-binding proteins in bacteria. A problematic challenge in the crystallization of LysR-type regulators stems from the insolubility and precipitation difficulties encountered with high concentrations of the full-length versions of these proteins. A general oligomerization scheme is proposed for this protein family based on the structures of the effector-binding domain of BenM in two different space groups, P4(3)22 and C222(1). These structures used the same oligomerization scheme of dimer-dimer interactions as another LysR-type regulator, CbnR, the full-length structure of which is available [Muraoka et al. (2003), J. Mol. Biol. 328, 555-566]. Evaluation of packing relationships and surface features suggests that BenM can form infinite oligomeric arrays in crystals through these dimer-dimer interactions. By extrapolation to the liquid phase, such dimer-dimer interactions may contribute to the significant difficulty in crystallizing full-length members of this family. The oligomerization of dimeric units to form biologically important tetramers appears to leave unsatisfied oligomerization sites. Under conditions that favor association, such as neutral pH and concentrations appropriate for crystallization, higher order oligomerization could cause solubility problems with purified proteins. A detailed model by which BenM and other LysR-type transcriptional regulators may form these arrays is proposed.

	~~{{STRUCTURE_2f8d\| PDB=2f8d \| SCENE= }}~~		Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.,Ezezika OC, Haddad S, Neidle EL, Momany C Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 May 1;63(Pt, 5):361-8. Epub 2007 Apr 28. PMID:17565172<ref>PMID:17565172</ref>

	~~===BenM effector-Binding domain crystallized from high pH conditions===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17565172}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2f8d]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017565172<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Acinetobacter baylyi]]		[[Category: Acinetobacter baylyi]]
	[[Category: Ezezika, O C.]]		[[Category: Ezezika, O C.]]

OCA: Protected "2f8d" [edit=sysop:move=sysop]

2013-01-07T12:49:08Z

Protected "2f8d" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:49, 7 January 2013
(No difference)

OCA at 12:49, 7 January 2013

2013-01-07T12:49:06Z

← Older revision		Revision as of 12:49, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2f8d.png\|left\|200px]]		[[Image:2f8d.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2f8d", 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_2f8d\| PDB=2f8d \| SCENE= }}		{{STRUCTURE_2f8d\| PDB=2f8d \| SCENE= }}

	===BenM effector-Binding domain crystallized from high pH conditions===		===BenM effector-Binding domain crystallized from high pH conditions===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17565172}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17565172 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17565172}}		{{ABSTRACT_PUBMED_17565172}}

	==About this Structure==		==About this Structure==
	~~2F8D~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA].		[[2f8d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17565172~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017565172</ref><references group="xtra"/>
	[[Category: Acinetobacter baylyi]]		[[Category: Acinetobacter baylyi]]
	[[Category: Ezezika, O C.]]		[[Category: Ezezika, O C.]]
Line 36:		Line 24:
	[[Category: Lysr-type transcriptional regulator]]		[[Category: Lysr-type transcriptional regulator]]
	[[Category: Tetramerization]]		[[Category: Tetramerization]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Sep 10 13:31:43 2010''~~

OCA at 09:23, 10 September 2010

2010-09-10T09:23:13Z

← Older revision		Revision as of 09:23, 10 September 2010
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	===BenM effector-Binding domain crystallized from high pH conditions===		===BenM effector-Binding domain crystallized from high pH conditions===


			<!--
			The line below this paragraph, {{ABSTRACT_PUBMED_17565172}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 17565172 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_17565172}}

	==About this Structure==		==About this Structure==
	2F8D is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA].		2F8D is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA].

			==Reference==
			<ref group="xtra">PMID:17565172</ref><references group="xtra"/>
	[[Category: Acinetobacter baylyi]]		[[Category: Acinetobacter baylyi]]
	[[Category: Ezezika, O C.]]		[[Category: Ezezika, O C.]]
	[[Category: Haddad, S.]]		[[Category: Haddad, S.]]
	[[Category: Momany, C.]]		[[Category: Momany, C.]]
	[[Category: Neidle, E.]]		[[Category: Neidle, E L.]]
	[[Category: Benm]]		[[Category: Benm]]
	[[Category: Effector binding domain]]		[[Category: Effector binding domain]]
			[[Category: Gene regulation]]
	[[Category: Inducer binding domain]]		[[Category: Inducer binding domain]]
	[[Category: Lttr]]		[[Category: Lttr]]
Line 27:		Line 37:
	[[Category: Tetramerization]]		[[Category: Tetramerization]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Feb 18 06~~:54:~~27 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Sep 10 13:31:43 2010''

OCA at 04:54, 18 February 2009

2009-02-18T04:54:29Z

← Older revision		Revision as of 04:54, 18 February 2009
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	[[Image:2f8d.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:2f8d.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2f8d\| PDB=2f8d \| SCENE= }}		{{STRUCTURE_2f8d\| PDB=2f8d \| SCENE= }}

	~~'''~~BenM effector-Binding domain crystallized from high pH conditions~~'''~~		===BenM effector-Binding domain crystallized from high pH conditions===


	==About this Structure==		==About this Structure==
	2F8D is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA].		2F8D is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8D OCA].
	[[Category: Acinetobacter baylyi]]		[[Category: Acinetobacter baylyi]]
	~~[[Category: Single protein]]~~
	[[Category: Ezezika, O C.]]		[[Category: Ezezika, O C.]]
	[[Category: Haddad, S.]]		[[Category: Haddad, S.]]
Line 26:		Line 26:
	[[Category: Lysr-type transcriptional regulator]]		[[Category: Lysr-type transcriptional regulator]]
	[[Category: Tetramerization]]		[[Category: Tetramerization]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 03~~:35:~~03 2008~~''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:54:27 2009''