4jl3 - Revision history

OCA at 10:44, 31 August 2022

2022-08-31T10:44:50Z

←Older revision		Revision as of 10:44, 31 August 2022
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	==Crystal structure of ms6564-dna complex==		==Crystal structure of ms6564-dna complex==
-	<StructureSection load='4jl3' size='340' side='right'caption='[[4jl3]]~~, [[Resolution\|resolution]] 2.50Å~~' scene=''>	+	<StructureSection load='4jl3' size='340' side='right'caption='[[4jl3]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[4jl3]] is a 6 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JL3 FirstGlance]. <br>
-	</td></tr>~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jl3 OCA], [https://pdbe.org/4jl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jl3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jl3 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4jkz\|4jkz]]</div></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=4jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jl3 OCA], [https://pdbe.org/4jl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jl3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jl3 ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Master regulators, which broadly affect expression of diverse genes, play critical roles in bacterial growth and environmental adaptation. However, the underlying mechanism by which such regulators interact with their cognate DNA remains to be elucidated. In this study, we solved the crystal structure of a broad regulator Ms6564 in Mycobacterium smegmatis and its protein-operator complex at resolutions of 1.9 and 2.5 A, respectively. Similar to other typical TetR family regulators, two dimeric Ms6564 molecules were found to bind to opposite sides of target DNA. However, the recognition helix of Ms6564 inserted only slightly into the DNA major groove. Unexpectedly, 11 disordered water molecules bridged the interface of TetR family regulator DNA. Although the DNA was deformed upon Ms6564 binding, it still retained the conformation of B-form DNA. Within the DNA-binding domain of Ms6564, only two amino acids residues directly interacted with the bases of cognate DNA. Lys-47 was found to be essential for the specific DNA binding ability of Ms6564. These data indicate that Ms6564 can bind DNA with strong affinity but makes flexible contacts with DNA. Our study suggests that Ms6564 might slide more easily along the genomic DNA and extensively regulate the expression of diverse genes in M. smegmatis.
-
-	Structural basis for interaction between Mycobacterium smegmatis Ms6564, a TetR family master regulator, and its target DNA.,Yang S, Gao Z, Li T, Yang M, Zhang T, Dong Y, He ZG J Biol Chem. 2013 Aug 16;288(33):23687-95. doi: 10.1074/jbc.M113.468694. Epub, 2013 Jun 26. PMID:23803605<ref>PMID:23803605</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4jl3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]		*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dong~~, Y H~~]]	+	[[Category: Dong YH]]
-	[[Category: Gao~~, Z Q~~]]	+	[[Category: Gao ZQ]]
-	[[Category: He~~, Z G~~]]	+	[[Category: He ZG]]
-	[[Category: Yang~~, S F]]~~	+	[[Category: Yang SF]]
-	~~[[Category: Transcription regulator]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 05:02, 25 August 2022

2022-08-25T05:02:50Z

←Older revision		Revision as of 05:02, 25 August 2022
Line 1:		Line 1:

	==Crystal structure of ms6564-dna complex==		==Crystal structure of ms6564-dna complex==
-	<StructureSection load='4jl3' size='340' side='right' caption='[[4jl3]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4jl3' size='340' side='right'caption='[[4jl3]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jl3]] is a 6 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jl3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JL3 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">~~[[4jkz\|4jkz]]~~<~~/td></tr>~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4jkz\|4jkz]]</div></td></tr>
-	~~<tr id~~='~~gene~~'~~><td class="sblockLbl"><b~~>[[~~Gene~~\|~~Gene:~~]]</b>~~</td><td class="sblockDat">MSMEG_6564, MSMEI_6387 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])~~</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=4jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jl3 OCA], [https://pdbe.org/4jl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jl3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jl3 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=4jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jl3 OCA], [~~http~~://pdbe.org/4jl3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jl3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jl3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jl3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Master regulators, which broadly affect expression of diverse genes, play critical roles in bacterial growth and environmental adaptation. However, the underlying mechanism by which such regulators interact with their cognate DNA remains to be elucidated. In this study, we solved the crystal structure of a broad regulator Ms6564 in Mycobacterium smegmatis and its protein-operator complex at resolutions of 1.9 and 2.5 A, respectively. Similar to other typical TetR family regulators, two dimeric Ms6564 molecules were found to bind to opposite sides of target DNA. However, the recognition helix of Ms6564 inserted only slightly into the DNA major groove. Unexpectedly, 11 disordered water molecules bridged the interface of TetR family regulator DNA. Although the DNA was deformed upon Ms6564 binding, it still retained the conformation of B-form DNA. Within the DNA-binding domain of Ms6564, only two amino acids residues directly interacted with the bases of cognate DNA. Lys-47 was found to be essential for the specific DNA binding ability of Ms6564. These data indicate that Ms6564 can bind DNA with strong affinity but makes flexible contacts with DNA. Our study suggests that Ms6564 might slide more easily along the genomic DNA and extensively regulate the expression of diverse genes in M. smegmatis.
		+
		+	Structural basis for interaction between Mycobacterium smegmatis Ms6564, a TetR family master regulator, and its target DNA.,Yang S, Gao Z, Li T, Yang M, Zhang T, Dong Y, He ZG J Biol Chem. 2013 Aug 16;288(33):23687-95. doi: 10.1074/jbc.M113.468694. Epub, 2013 Jun 26. PMID:23803605<ref>PMID:23803605</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4jl3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mycs2~~]]	+	[[Category: Large Structures]]
	[[Category: Dong, Y H]]		[[Category: Dong, Y H]]
	[[Category: Gao, Z Q]]		[[Category: Gao, Z Q]]

OCA at 23:55, 4 August 2016

2016-08-04T23:55:53Z

←Older revision		Revision as of 23:55, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of ms6564-dna complex==		==Crystal structure of ms6564-dna complex==
	<StructureSection load='4jl3' size='340' side='right' caption='[[4jl3]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4jl3' size='340' side='right' caption='[[4jl3]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jl3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jl3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JL3 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jkz\|4jkz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jkz\|4jkz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_6564, MSMEI_6387 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 ~~Mycobacterium smegmatis str. MC2 155~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_6564, MSMEI_6387 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=4jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jl3 RCSB], [http://www.ebi.ac.uk/pdbsum/4jl3 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=4jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jl3 OCA], [http://pdbe.org/4jl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jl3 RCSB], [http://www.ebi.ac.uk/pdbsum/4jl3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jl3 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mycobacterium smegmatis str. mc2 155~~]]	+	[[Category: Mycs2]]
	[[Category: Dong, Y H]]		[[Category: Dong, Y H]]
	[[Category: Gao, Z Q]]		[[Category: Gao, Z Q]]

OCA at 14:28, 21 December 2014

2014-12-21T14:28:45Z

←Older revision		Revision as of 14:28, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4jl3\| PDB=4jl3 \| SCENE= }}~~	+	==Crystal structure of ms6564-dna complex==
-	===Crystal structure of ms6564-dna complex===	+	<StructureSection load='4jl3' size='340' side='right' caption='[[4jl3]], [[Resolution\|resolution]] 2.50Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[4jl3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JL3 FirstGlance]. <br>
-	[[4jl3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA].	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jkz\|4jkz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_6564, MSMEI_6387 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 Mycobacterium smegmatis str. MC2 155])</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=4jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jl3 RCSB], [http://www.ebi.ac.uk/pdbsum/4jl3 PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium smegmatis str. mc2 155]]		[[Category: Mycobacterium smegmatis str. mc2 155]]
-	[[Category: Dong, Y H.]]	+	[[Category: Dong, Y H]]
-	[[Category: Gao, Z Q.]]	+	[[Category: Gao, Z Q]]
-	[[Category: He, Z G.]]	+	[[Category: He, Z G]]
-	[[Category: Yang, S F.]]	+	[[Category: Yang, S F]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 10:29, 30 June 2013

2013-06-30T10:29:07Z

←Older revision		Revision as of 10:29, 30 June 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jl3\| PDB=4jl3 \| SCENE= }}
		+	===Crystal structure of ms6564-dna complex===

-	~~The entry~~ 4jl3 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4jl3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JL3 OCA].
-	~~Authors~~: ~~Yang~~, ~~S.F~~., Gao, Z.Q., ~~Dong~~, ~~Y.H~~.	+	[[Category: Mycobacterium smegmatis str. mc2 155]]
-		+	[[Category: Dong, Y H.]]
-	~~Description~~: ~~Crystal structure of ms6564~~-dna complex	+	[[Category: Gao, Z Q.]]
		+	[[Category: He, Z G.]]
		+	[[Category: Yang, S F.]]
		+	[[Category: Transcription regulator]]
		+	[[Category: Transcription-dna complex]]

OCA at 19:55, 17 April 2013

2013-04-17T19:55:18Z

←Older revision		Revision as of 19:55, 17 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4jl3 is ON HOLD	+	The entry 4jl3 is ON HOLD until Paper Publication

	Authors: Yang, S.F., Gao, Z.Q., Dong, Y.H.		Authors: Yang, S.F., Gao, Z.Q., Dong, Y.H.

	Description: Crystal structure of ms6564-dna complex		Description: Crystal structure of ms6564-dna complex

OCA at 08:18, 27 March 2013

2013-03-27T08:18:29Z

←Older revision		Revision as of 08:18, 27 March 2013
Line 5:		Line 5:
	Authors: Yang, S.F., Gao, Z.Q., Dong, Y.H.		Authors: Yang, S.F., Gao, Z.Q., Dong, Y.H.

-	Description: ~~crystal~~ structure of ms6564-dna complex	+	Description: Crystal structure of ms6564-dna complex

OCA: Protected "4jl3" [edit=sysop:move=sysop]

2013-03-20T16:22:00Z

Protected "4jl3" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:22, 20 March 2013

OCA: New page: '''Unreleased structure''' The entry 4jl3 is ON HOLD Authors: Yang, S.F., Gao, Z.Q., Dong, Y.H. Description: crystal structure of ms6564-dna complex

2013-03-20T16:21:59Z

New page: '''Unreleased structure''' The entry 4jl3 is ON HOLD Authors: Yang, S.F., Gao, Z.Q., Dong, Y.H. Description: crystal structure of ms6564-dna complex

New page

'''Unreleased structure'''

The entry 4jl3 is ON HOLD

Authors: Yang, S.F., Gao, Z.Q., Dong, Y.H.

Description: crystal structure of ms6564-dna complex