4if4 - Revision history

OCA at 11:55, 1 March 2024

OCA — Fri, 01 Mar 2024 11:55:05 GMT

←Older revision		Revision as of 11:55, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4if4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IF4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4if4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IF4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4if4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4if4 OCA], [https://pdbe.org/4if4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4if4 RCSB], [https://www.ebi.ac.uk/pdbsum/4if4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4if4 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=4if4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4if4 OCA], [https://pdbe.org/4if4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4if4 RCSB], [https://www.ebi.ac.uk/pdbsum/4if4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4if4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/VRAR_STAAM VRAR_STAAM] Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. VraR is overexpressed in strain Mu50, which leads to vancomycin resistance.		[https://www.uniprot.org/uniprot/VRAR_STAAM VRAR_STAAM] Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. VraR is overexpressed in strain Mu50, which leads to vancomycin resistance.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Staphylococcus aureus VraR, a vancomycin-resistance-associated response regulator, activates a cell-wall-stress stimulon in response to antibiotics that inhibit cell wall formation. X-ray crystal structures of VraR in both unphosphorylated and beryllofluoride-activated states have been determined, revealing a mechanism of phosphorylation-induced dimerization that features a deep hydrophobic pocket at the center of the receiver domain interface. Unphosphorylated VraR exists in a closed conformation that inhibits dimer formation. Phosphorylation at the active site promotes conformational changes that are propagated throughout the receiver domain, promoting the opening of a hydrophobic pocket that is essential for homodimer formation and enhanced DNA-binding activity. This prominent feature in the VraR dimer can potentially be exploited for the development of novel therapeutics to counteract antibiotic resistance in this important pathogen.
-
-	Phosphorylation-dependent conformational changes and domain rearrangements in Staphylococcus aureus VraR activation.,Leonard PG, Golemi-Kotra D, Stock AM Proc Natl Acad Sci U S A. 2013 May 21;110(21):8525-30. doi:, 10.1073/pnas.1302819110. Epub 2013 May 6. PMID:23650349<ref>PMID:23650349</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4if4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Response regulator 3D structure\|Response regulator 3D structure]]		*[[Response regulator 3D structure\|Response regulator 3D structure]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:06, 9 November 2022

OCA — Wed, 09 Nov 2022 09:06:06 GMT

←Older revision		Revision as of 09:06, 9 November 2022
Line 1:		Line 1:

	==Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus==		==Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus==
-	<StructureSection load='4if4' size='340' side='right' caption='[[4if4]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='4if4' size='340' side='right'caption='[[4if4]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4if4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staam Staam~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IF4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4if4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IF4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[4gvp\|4gvp]]</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=4if4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4if4 OCA], [https://pdbe.org/4if4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4if4 RCSB], [https://www.ebi.ac.uk/pdbsum/4if4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4if4 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAV1884, vraR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])~~</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=4if4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4if4 OCA], [~~http~~://pdbe.org/4if4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4if4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4if4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4if4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VRAR_STAAM VRAR_STAAM]] Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. VraR is overexpressed in strain Mu50, which leads to vancomycin resistance.	+	[https://www.uniprot.org/uniprot/VRAR_STAAM VRAR_STAAM] Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. VraR is overexpressed in strain Mu50, which leads to vancomycin resistance.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Response regulator\|Response regulator]]	+	*[[Response regulator 3D structure\|Response regulator 3D structure]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staam~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Leonard, P G~~]]	+	[[Category: Staphylococcus aureus subsp. aureus Mu50]]
-	[[Category: ~~Stock, A M~~]]	+	[[Category: Leonard PG]]
-	[[Category: ~~Bacterial signalling]]~~	+	[[Category: Stock AM]]
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Response regulator]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Two-component system~~]]	+

OCA at 16:20, 5 August 2016

OCA — Fri, 05 Aug 2016 16:20:10 GMT

←Older revision		Revision as of 16:20, 5 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4if4\| PDB=4if4 \| SCENE= }}
-	===Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus===
-	{{ABSTRACT_PUBMED_23650349}}

-	==~~About this~~ Structure==	+	==Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus==
-	[[4if4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus_subsp._aureus_mu50 Staphylococcus aureus subsp. aureus mu50~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA].	+	<StructureSection load='4if4' size='340' side='right' caption='[[4if4]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4if4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staam Staam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IF4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[4gvp\|4gvp]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAV1884, vraR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])</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=4if4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4if4 OCA], [http://pdbe.org/4if4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4if4 RCSB], [http://www.ebi.ac.uk/pdbsum/4if4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4if4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VRAR_STAAM VRAR_STAAM]] Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. VraR is overexpressed in strain Mu50, which leads to vancomycin resistance.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Staphylococcus aureus VraR, a vancomycin-resistance-associated response regulator, activates a cell-wall-stress stimulon in response to antibiotics that inhibit cell wall formation. X-ray crystal structures of VraR in both unphosphorylated and beryllofluoride-activated states have been determined, revealing a mechanism of phosphorylation-induced dimerization that features a deep hydrophobic pocket at the center of the receiver domain interface. Unphosphorylated VraR exists in a closed conformation that inhibits dimer formation. Phosphorylation at the active site promotes conformational changes that are propagated throughout the receiver domain, promoting the opening of a hydrophobic pocket that is essential for homodimer formation and enhanced DNA-binding activity. This prominent feature in the VraR dimer can potentially be exploited for the development of novel therapeutics to counteract antibiotic resistance in this important pathogen.

-	~~==Reference==~~	+	Phosphorylation-dependent conformational changes and domain rearrangements in Staphylococcus aureus VraR activation.,Leonard PG, Golemi-Kotra D, Stock AM Proc Natl Acad Sci U S A. 2013 May 21;110(21):8525-30. doi:, 10.1073/pnas.1302819110. Epub 2013 May 6. PMID:23650349<ref>PMID:23650349</ref>
-	<ref ~~group="xtra"~~>PMID:~~023650349~~</ref><~~references group~~="~~xtra~~"/><references/>	+
-	[[Category: ~~Staphylococcus aureus subsp. aureus mu50~~]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Leonard, P G.]]	+	</div>
-	[[Category: Stock, A M.]]	+	<div class="pdbe-citations 4if4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Response regulator\|Response regulator]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Staam]]
		+	[[Category: Leonard, P G]]
		+	[[Category: Stock, A M]]
	[[Category: Bacterial signalling]]		[[Category: Bacterial signalling]]
	[[Category: Dna binding]]		[[Category: Dna binding]]

OCA at 07:52, 19 June 2013

OCA — Wed, 19 Jun 2013 07:52:56 GMT

←Older revision		Revision as of 07:52, 19 June 2013
Line 1:		Line 1:
	{{STRUCTURE_4if4\| PDB=4if4 \| SCENE= }}		{{STRUCTURE_4if4\| PDB=4if4 \| SCENE= }}
	===Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus===		===Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus===
		+	{{ABSTRACT_PUBMED_23650349}}

	==About this Structure==		==About this Structure==
	[[4if4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_mu50 Staphylococcus aureus subsp. aureus mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA].		[[4if4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_mu50 Staphylococcus aureus subsp. aureus mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023650349</ref><references group="xtra"/><references/>
	[[Category: Staphylococcus aureus subsp. aureus mu50]]		[[Category: Staphylococcus aureus subsp. aureus mu50]]
	[[Category: Leonard, P G.]]		[[Category: Leonard, P G.]]

OCA at 07:54, 8 May 2013

OCA — Wed, 08 May 2013 07:54:57 GMT

←Older revision		Revision as of 07:54, 8 May 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4if4\| PDB=4if4 \| SCENE= }}
		+	===Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus===

-	~~The entry~~ 4if4 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4if4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_mu50 Staphylococcus aureus subsp. aureus mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA].
-	~~Authors~~: Leonard, P.G., Stock, A.M.	+	[[Category: Staphylococcus aureus subsp. aureus mu50]]
-		+	[[Category: Leonard, P G.]]
-	~~Description~~: ~~Crystal Structure of the Magnesium and beryllofluoride~~-~~activated VraR from Staphylococcus aureus~~	+	[[Category: Stock, A M.]]
		+	[[Category: Bacterial signalling]]
		+	[[Category: Dna binding]]
		+	[[Category: Phosphorylation]]
		+	[[Category: Response regulator]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Two-component system]]

OCA at 19:49, 17 April 2013

OCA — Wed, 17 Apr 2013 19:49:42 GMT

←Older revision		Revision as of 19:49, 17 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4if4 is ON HOLD	+	The entry 4if4 is ON HOLD until Paper Publication

	Authors: Leonard, P.G., Stock, A.M.		Authors: Leonard, P.G., Stock, A.M.

	Description: Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus		Description: Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus

OCA: Protected "4if4" [edit=sysop:move=sysop]

OCA — Wed, 19 Dec 2012 11:09:58 GMT

Protected "4if4" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:09, 19 December 2012

OCA: New page: '''Unreleased structure''' The entry 4if4 is ON HOLD Authors: Leonard, P.G., Stock, A.M. Description: Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphyl...

OCA — Wed, 19 Dec 2012 11:09:57 GMT

New page: '''Unreleased structure''' The entry 4if4 is ON HOLD Authors: Leonard, P.G., Stock, A.M. Description: Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphyl...

New page

'''Unreleased structure'''

The entry 4if4 is ON HOLD

Authors: Leonard, P.G., Stock, A.M.

Description: Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus