5gpa - Revision history

OCA at 11:38, 2 August 2023

OCA — Wed, 02 Aug 2023 11:38:38 GMT

←Older revision		Revision as of 11:38, 2 August 2023
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	==Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans==		==Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans==
-	<StructureSection load='5gpa' size='340' side='right' caption='[[5gpa]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5gpa' size='340' side='right'caption='[[5gpa]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gpa]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bachd Bachd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gpa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GPA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.051Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5gp9\|5gp9]], [[5gpc\|5gpc]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BH3102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272558 BACHD])~~</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=5gpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpa OCA], [https://pdbe.org/5gpa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gpa RCSB], [https://www.ebi.ac.uk/pdbsum/5gpa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpa 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=5gpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpa OCA], [~~http~~://pdbe.org/5gpa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gpa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gpa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpa ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9K8A4_HALH5 Q9K8A4_HALH5]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5gpa" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gpa" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bachd~~]]	+	[[Category: Alkalihalobacillus halodurans C-125]]
-	[[Category: ~~Lee, J Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Park, Y W~~]]	+	[[Category: Lee JY]]
-	[[Category: ~~Yeo, H K~~]]	+	[[Category: Park YW]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Yeo HK]]
-	~~[[Category: Fadr]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcriptional regulator~~]]	+

OCA at 07:33, 6 December 2017

OCA — Wed, 06 Dec 2017 07:33:45 GMT

←Older revision		Revision as of 07:33, 6 December 2017
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	<StructureSection load='5gpa' size='340' side='right' caption='[[5gpa]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5gpa' size='340' side='right' caption='[[5gpa]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gpa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gpa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bachd Bachd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GPA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gp9\|5gp9]], [[5gpc\|5gpc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gp9\|5gp9]], [[5gpc\|5gpc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BH3102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272558 BACHD])</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=5gpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpa OCA], [http://pdbe.org/5gpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gpa RCSB], [http://www.ebi.ac.uk/pdbsum/5gpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpa 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=5gpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpa OCA], [http://pdbe.org/5gpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gpa RCSB], [http://www.ebi.ac.uk/pdbsum/5gpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpa ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	FadR is a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. In this study, the crystal structures of Bacillus halodurans FadR, which belong to the TetR family, have been determined in three different forms: ligand-bound, ligand-free and DNA-bound at resolutions of 1.75, 2.05 and 2.80 A, respectively. Structural and functional data showed that B. halodurans FadR was bound to its operator site without fatty acyl-CoAs. Structural comparisons among the three different forms of B. halodurans FadR revealed that the movement of DNA binding domains toward the operator DNA was blocked upon binding of ligand molecules. These findings suggest that the TetR family FadR negatively regulates the genes involved in fatty acid metabolism by binding cooperatively to the operator DNA as a dimer of dimers.
		+
		+	Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR.,Yeo HK, Park YW, Lee JY Nucleic Acids Res. 2017 Apr 20;45(7):4244-4254. doi: 10.1093/nar/gkx009. PMID:28160603<ref>PMID:28160603</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gpa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bachd]]
	[[Category: Lee, J Y]]		[[Category: Lee, J Y]]
	[[Category: Park, Y W]]		[[Category: Park, Y W]]

OCA at 09:31, 11 March 2017

OCA — Sat, 11 Mar 2017 09:31:59 GMT

←Older revision		Revision as of 09:31, 11 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gpa is ~~ON HOLD until Paper Publication~~	+	==Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans==
-		+	<StructureSection load='5gpa' size='340' side='right' caption='[[5gpa]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~Authors~~: ~~Lee~~, J.Y., ~~Yeo~~, H.K., ~~Park~~, Y.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5gpa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GPA FirstGlance]. <br>
-	~~Description: Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gp9\|5gp9]], [[5gpc\|5gpc]]</td></tr>
-	[[Category: Park, Y.W]]	+	<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=5gpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpa OCA], [http://pdbe.org/5gpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gpa RCSB], [http://www.ebi.ac.uk/pdbsum/5gpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpa ProSAT]</span></td></tr>
-	[[Category: Yeo, H.K]]	+	</table>
-	[[Category: ~~Lee, J.Y~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Lee, J Y]]
		+	[[Category: Park, Y W]]
		+	[[Category: Yeo, H K]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Fadr]]
		+	[[Category: Transcription]]
		+	[[Category: Transcriptional regulator]]

OCA at 11:54, 9 September 2016

OCA — Fri, 09 Sep 2016 11:54:03 GMT

←Older revision		Revision as of 11:54, 9 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5gpa is ON HOLD	+	The entry 5gpa is ON HOLD until Paper Publication

	Authors: Lee, J.Y., Yeo, H.K., Park, Y.W.		Authors: Lee, J.Y., Yeo, H.K., Park, Y.W.

OCA: Protected "5gpa" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2016 11:08:57 GMT

Protected "5gpa" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:08, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5gpa is ON HOLD Authors: Lee, J.Y., Yeo, H.K., Park, Y.W. Description: Structural analysis of fatty acid degradation regulator FadR from Bacillus h...

OCA — Wed, 10 Aug 2016 11:08:55 GMT

New page: '''Unreleased structure''' The entry 5gpa is ON HOLD Authors: Lee, J.Y., Yeo, H.K., Park, Y.W. Description: Structural analysis of fatty acid degradation regulator FadR from Bacillus h...

New page

'''Unreleased structure'''

The entry 5gpa is ON HOLD

Authors: Lee, J.Y., Yeo, H.K., Park, Y.W.

Description: Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans
[[Category: Unreleased Structures]]
[[Category: Park, Y.W]]
[[Category: Yeo, H.K]]
[[Category: Lee, J.Y]]