4wt0 - Revision history

OCA at 00:55, 28 December 2023

2023-12-28T00:55:25Z

←Older revision		Revision as of 00:55, 28 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</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=4wt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wt0 OCA], [https://pdbe.org/4wt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wt0 RCSB], [https://www.ebi.ac.uk/pdbsum/4wt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wt0 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=4wt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wt0 OCA], [https://pdbe.org/4wt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wt0 RCSB], [https://www.ebi.ac.uk/pdbsum/4wt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wt0 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:24, 7 April 2023

2023-04-07T07:24:48Z

←Older revision		Revision as of 07:24, 7 April 2023
Line 3:		Line 3:
	<StructureSection load='4wt0' size='340' side='right'caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4wt0' size='340' side='right'caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis_s613 Enterococcus faecalis s613]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wsz\|4wsz]], [[4wu4\|4wu4]], [[4wuh\|4wuh]], [[4wul\|4wul]]~~</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=4wt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wt0 OCA], [https://pdbe.org/4wt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wt0 RCSB], [https://www.ebi.ac.uk/pdbsum/4wt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wt0 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=4wt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wt0 OCA], [~~http~~://pdbe.org/4wt0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wt0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wt0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wt0 ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
		+	*[[Aspartate carbamoyltransferase 3D structures\|Aspartate carbamoyltransferase 3D structures]]
	*[[Response regulator 3D structure\|Response regulator 3D structure]]		*[[Response regulator 3D structure\|Response regulator 3D structure]]
	== References ==		== References ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Enterococcus faecalis s613]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davlieva, M]]	+	[[Category: Davlieva M]]
-	[[Category: Shamoo, Y]]	+	[[Category: Shamoo Y]]
-	~~[[Category: Daptomycin resistant mutation]]~~	+
-	~~[[Category: Dna binding domain]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Helix-turn-helix]]~~	+
-	~~[[Category: Response regulator~~]]	+

OCA at 15:46, 11 December 2019

2019-12-11T15:46:05Z

←Older revision		Revision as of 15:46, 11 December 2019
Line 1:		Line 1:

	==Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis==		==Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis==
-	<StructureSection load='4wt0' size='340' side='right' caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4wt0' size='340' side='right'caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis_s613 Enterococcus faecalis s613]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis_s613 Enterococcus faecalis s613]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4wt0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4wt0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Response regulator 3D structure\|Response regulator 3D structure]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Enterococcus faecalis s613]]		[[Category: Enterococcus faecalis s613]]
		+	[[Category: Large Structures]]
	[[Category: Davlieva, M]]		[[Category: Davlieva, M]]
	[[Category: Shamoo, Y]]		[[Category: Shamoo, Y]]

OCA at 15:16, 15 November 2017

2017-11-15T15:16:37Z

←Older revision		Revision as of 15:16, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='4wt0' size='340' side='right' caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4wt0' size='340' side='right' caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis_s613 Enterococcus faecalis s613]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wsz\|4wsz]], [[4wu4\|4wu4]], [[4wuh\|4wuh]], [[4wul\|4wul]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wsz\|4wsz]], [[4wu4\|4wu4]], [[4wuh\|4wuh]], [[4wul\|4wul]]</td></tr>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4wt0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4wt0" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Response regulator\|Response regulator]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterococcus faecalis s613]]
	[[Category: Davlieva, M]]		[[Category: Davlieva, M]]
	[[Category: Shamoo, Y]]		[[Category: Shamoo, Y]]

OCA at 01:56, 10 March 2017

2017-03-10T01:56:34Z

←Older revision		Revision as of 01:56, 10 March 2017
Line 1:		Line 1:
		+
	==Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis==		==Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis==
	<StructureSection load='4wt0' size='340' side='right' caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4wt0' size='340' side='right' caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wsz\|4wsz]], [[4wu4\|4wu4]], [[4wuh\|4wuh]], [[4wul\|4wul]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wsz\|4wsz]], [[4wu4\|4wu4]], [[4wuh\|4wuh]], [[4wul\|4wul]]</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=4wt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wt0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wt0 RCSB], [http://www.ebi.ac.uk/pdbsum/4wt0 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=4wt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wt0 OCA], [http://pdbe.org/4wt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wt0 RCSB], [http://www.ebi.ac.uk/pdbsum/4wt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wt0 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4wt0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 06:47, 3 June 2015

2015-06-03T06:47:02Z

←Older revision		Revision as of 06:47, 3 June 2015
Line 15:		Line 15:
	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>
		+
		+	==See Also==
		+	*[[Response regulator\|Response regulator]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:50, 6 May 2015

2015-05-06T12:50:18Z

←Older revision		Revision as of 12:50, 6 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis==
		+	<StructureSection load='4wt0' size='340' side='right' caption='[[4wt0]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4wt0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WT0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wsz\|4wsz]], [[4wu4\|4wu4]], [[4wuh\|4wuh]], [[4wul\|4wul]]</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=4wt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wt0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wt0 RCSB], [http://www.ebi.ac.uk/pdbsum/4wt0 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LiaR is a 'master regulator' of the cell envelope stress response in enterococci and many other Gram-positive organisms. Mutations to liaR can lead to antibiotic resistance to a variety of antibiotics including the cyclic lipopeptide daptomycin. LiaR is phosphorylated in response to membrane stress to regulate downstream target operons. Using DNA footprinting of the regions upstream of the liaXYZ and liaFSR operons we show that LiaR binds an extended stretch of DNA that extends beyond the proposed canonical consensus sequence suggesting a more complex level of regulatory control of target operons. We go on to determine the biochemical and structural basis for increased resistance to daptomycin by the adaptive mutation to LiaR (D191N) first identified from the pathogen Enterococcus faecalis S613. LiaRD191N increases oligomerization of LiaR to form a constitutively activated tetramer that has high affinity for DNA even in the absence of phosphorylation leading to increased resistance. Crystal structures of the LiaR DNA binding domain complexed to the putative consensus sequence as well as an adjoining secondary sequence show that upon binding, LiaR induces DNA bending that is consistent with increased recruitment of RNA polymerase to the transcription start site and upregulation of target operons.

-	~~The entry 4wt0 is ON HOLD until Paper Publication~~	+	A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin.,Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR, Arias CA, Ladbury JE, Shamoo Y Nucleic Acids Res. 2015 Apr 19. pii: gkv321. PMID:25897118<ref>PMID:25897118</ref>

-	~~Authors: Davlieva~~, M.~~, Shamoo, Y~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure~~ of ~~the DNA binding domains of LiaRD191N from E~~. ~~faecalis~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Davlieva, M]]
	[[Category: Shamoo, Y]]		[[Category: Shamoo, Y]]
-	[[Category: ~~Davlieva, M~~]]	+	[[Category: Daptomycin resistant mutation]]
		+	[[Category: Dna binding domain]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Helix-turn-helix]]
		+	[[Category: Response regulator]]

OCA at 19:56, 24 December 2014

2014-12-24T19:56:51Z

←Older revision		Revision as of 19:56, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis		Description: Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis
		+	[[Category: Unreleased Structures]]
		+	[[Category: Shamoo, Y]]
		+	[[Category: Davlieva, M]]

OCA at 11:56, 19 November 2014

2014-11-19T11:56:44Z

←Older revision		Revision as of 11:56, 19 November 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4wt0 is ON HOLD	+	The entry 4wt0 is ON HOLD until Paper Publication

	Authors: Davlieva, M., Shamoo, Y.		Authors: Davlieva, M., Shamoo, Y.

	Description: Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis		Description: Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis

OCA: Protected "4wt0" [edit=sysop:move=sysop]

2014-11-05T08:08:09Z

Protected "4wt0" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:08, 5 November 2014