4nb5 - Revision history

OCA at 12:32, 1 March 2024

2024-03-01T12:32:31Z

← Older revision		Revision as of 12:32, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nb5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NB5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nb5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NB5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</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]] 1.641Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</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=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [https://pdbe.org/4nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/4nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nb5 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=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [https://pdbe.org/4nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/4nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nb5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MMPR5_MYCTU MMPR5_MYCTU] Controls the expression level of the Mmps2-MmpL2, MmpS4-MmpL4, and MmpS5-MmpL5 transport systems. Also controls its own expression. Acts by binding directly to the promoter regions.<ref>PMID:18851927</ref> <ref>PMID:24590481</ref> <ref>PMID:24737322</ref>		[https://www.uniprot.org/uniprot/MMPR5_MYCTU MMPR5_MYCTU] Controls the expression level of the Mmps2-MmpL2, MmpS4-MmpL4, and MmpS5-MmpL5 transport systems. Also controls its own expression. Acts by binding directly to the promoter regions.<ref>PMID:18851927</ref> <ref>PMID:24590481</ref> <ref>PMID:24737322</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Recent work demonstrates that the Mycobacterial membrane protein large (MmpL) transporters are dedicated to the export of mycobacterial lipids for cell wall biosynthesis. An MmpL transporter frequently works with an accessory protein, belonging to the Mycobacterial membrane protein small (MmpS) family, to transport these key virulence factors. One such efflux system in Mycobacterium tuberculosis is the MmpS5-MmpL5 transporter. The expression of MmpS5-MmpL5 is controlled by the MarR-like transcriptional regulator Rv0678, whose open reading frame is located downstream of the mmpS5-mmpL5 operon. To elucidate the structural basis of Rv0678 regulation, we have determined the crystal structure of this regulator, to 1.64 angstrom resolution, revealing a dimeric two-domain molecule with an architecture similar to members of the MarR family of transcriptional regulators. Rv0678 is distinct from other MarR regulators in that its DNA-binding and dimerization domains are clustered together. These two domains seemingly cooperate to bind an inducing ligand that we identified as 2-palmitoylglycerol, which is a fatty acid glycerol ester. The structure also suggests that the conformational change leading to substrate-mediated derepression is primarily caused by a rigid body rotational motion of the entire DNA-binding domain of the regulator towards the dimerization domain. This movement results in a conformational state that is incompatible with DNA binding. We demonstrate using electrophoretic mobility shift assays that Rv0678 binds to the mmpS5-mmpL5, mmpS4-mmpL4 and the mmpS2-mmpL2 promoters. Binding by Rv0678 was reversed upon addition of the ligand. These findings provide new insight into the mechanisms of gene regulation in the MarR family of regulators.

	Crystal structure of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis.,Radhakrishnan A, Kumar N, Wright CC, Chou TH, Tringides ML, Bolla JR, Lei HT, Rajashankar K, Su CC, Purdy GE, Yu EW J Biol Chem. 2014 Apr 15. PMID:24737322<ref>PMID:24737322</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4nb5" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:19, 11 January 2023

2023-01-11T08:19:26Z

← Older revision		Revision as of 08:19, 11 January 2023
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	==Crystal Structure of a transcriptional regulator==		==Crystal Structure of a transcriptional regulator==
	<StructureSection load='4nb5' size='340' side='right' caption='[[4nb5]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='4nb5' size='340' side='right'caption='[[4nb5]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nb5]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NB5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nb5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NB5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0678, RVBD_0678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])~~</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=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [https://pdbe.org/4nb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [https://www.ebi.ac.uk/pdbsum/4nb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nb5 ProSAT]</span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [~~http~~://pdbe.org/4nb5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nb5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nb5 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/MMPR5_MYCTU MMPR5_MYCTU] Controls the expression level of the Mmps2-MmpL2, MmpS4-MmpL4, and MmpS5-MmpL5 transport systems. Also controls its own expression. Acts by binding directly to the promoter regions.<ref>PMID:18851927</ref> <ref>PMID:24590481</ref> <ref>PMID:24737322</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Myctu~~]]		[[Category: Large Structures]]
	[[Category: ~~Radhakrishnan, A~~]]		[[Category: Mycobacterium tuberculosis H37Rv]]
	[[Category: ~~Su, C C~~]]		[[Category: Radhakrishnan A]]
	[[Category: ~~Yu, E W~~]]		[[Category: Su C-C]]
	[[Category: ~~Dna binding]]~~		[[Category: Yu EW]]
	~~[[Category: Dna binding protein~~]]

OCA at 16:56, 11 August 2016

2016-08-11T16:56:25Z

← Older revision		Revision as of 16:56, 11 August 2016
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	==Crystal Structure of a transcriptional regulator==		==Crystal Structure of a transcriptional regulator==
	<StructureSection load='4nb5' size='340' side='right' caption='[[4nb5]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='4nb5' size='340' side='right' caption='[[4nb5]], [[Resolution\|resolution]] 1.64Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0678, RVBD_0678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0678, RVBD_0678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [http://www.ebi.ac.uk/pdbsum/4nb5 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=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [http://pdbe.org/4nb5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [http://www.ebi.ac.uk/pdbsum/4nb5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nb5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 4nb5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:18, 5 January 2015

2015-01-05T09:18:26Z

← Older revision		Revision as of 09:18, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nb5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NB5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nb5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NB5 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2JT:1,3-DIHYDROXYPROPAN-2-YL+OCTADECANOATE'>2JT</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0678, RVBD_0678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0678, RVBD_0678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [http://www.ebi.ac.uk/pdbsum/4nb5 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=4nb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nb5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nb5 RCSB], [http://www.ebi.ac.uk/pdbsum/4nb5 PDBsum]</span></td></tr>
	<table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Myctu]]		[[Category: Myctu]]
	[[Category: Radhakrishnan, A.]]		[[Category: Radhakrishnan, A]]
	[[Category: Su, C C.]]		[[Category: Su, C C]]
	[[Category: Yu, E W.]]		[[Category: Yu, E W]]
	[[Category: Dna binding]]		[[Category: Dna binding]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]

OCA at 05:41, 18 June 2014

2014-06-18T05:41:33Z

← Older revision		Revision as of 05:41, 18 June 2014
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	Crystal structure of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis.,Radhakrishnan A, Kumar N, Wright CC, Chou TH, Tringides ML, Bolla JR, Lei HT, Rajashankar K, Su CC, Purdy GE, Yu EW J Biol Chem. 2014 Apr 15. PMID:24737322<ref>PMID:24737322</ref>		Crystal structure of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis.,Radhakrishnan A, Kumar N, Wright CC, Chou TH, Tringides ML, Bolla JR, Lei HT, Rajashankar K, Su CC, Purdy GE, Yu EW J Biol Chem. 2014 Apr 15. PMID:24737322<ref>PMID:24737322</ref>

	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==

OCA at 07:02, 21 May 2014

2014-05-21T07:02:48Z

@@ Line 1: / Line 1: @@
-{{STRUCTURE_4nb5|  PDB=4nb5  |  SCENE=  }}
+==Crystal Structure of a transcriptional regulator==
-===Crystal Structure of a transcriptional regulator===
+<StructureSection load='4nb5' size='340' side='right' caption='[[4nb5]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
-==About this Structure==
+Crystal structure of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis.,Radhakrishnan A, Kumar N, Wright CC, Chou TH, Tringides ML, Bolla JR, Lei HT, Rajashankar K, Su CC, Purdy GE, Yu EW J Biol Chem. 2014 Apr 15. PMID:24737322<ref>PMID:24737322</ref>
-[[4nb5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA].
 [[Category: Radhakrishnan, A.]]
 [[Category: Su, C C.]]

OCA at 07:56, 23 April 2014

2014-04-23T07:56:58Z

← Older revision		Revision as of 07:56, 23 April 2014
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		{{STRUCTURE_4nb5\| PDB=4nb5 \| SCENE= }}
			===Crystal Structure of a transcriptional regulator===

	~~The entry~~ 4nb5 is ~~ON HOLD until Oct 22 2015~~		==About this Structure==
			[[4nb5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NB5 OCA].
	~~Authors~~: ~~Su, C~~.-C., Radhakrishnan, A., Yu, E.W.		[[Category: Radhakrishnan, A.]]
			[[Category: Su, C C.]]
	~~Description~~: ~~Crystal Structure of a transcriptional regulator~~		[[Category: Yu, E W.]]
			[[Category: Dna binding]]
			[[Category: Dna binding protein]]

OCA at 06:43, 22 January 2014

2014-01-22T06:43:57Z

← Older revision		Revision as of 06:43, 22 January 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4nb5 is ON HOLD		The entry 4nb5 is ON HOLD until Oct 22 2015

	Authors: Su, C.-C., Radhakrishnan, A., Yu, E.W.		Authors: Su, C.-C., Radhakrishnan, A., Yu, E.W.

	Description: Crystal Structure of a transcriptional regulator		Description: Crystal Structure of a transcriptional regulator

OCA at 07:42, 13 November 2013

2013-11-13T07:42:28Z

← Older revision		Revision as of 07:42, 13 November 2013
Line 3:		Line 3:
	The entry 4nb5 is ON HOLD		The entry 4nb5 is ON HOLD

	Authors: Su, C.-C., Radhakrishnan,A., Yu, E. W.		Authors: Su, C.-C., Radhakrishnan, A., Yu, E.W.

	Description: Crystal Structure of a transcriptional regulator		Description: Crystal Structure of a transcriptional regulator

OCA: Protected "4nb5" [edit=sysop:move=sysop]

2013-11-06T07:07:04Z

Protected "4nb5" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:07, 6 November 2013
(No difference)