3whb - Revision history

OCA at 08:45, 20 March 2024

OCA — Wed, 20 Mar 2024 08:45:11 GMT

←Older revision		Revision as of 08:45, 20 March 2024
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	<StructureSection load='3whb' size='340' side='right'caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3whb' size='340' side='right'caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WHB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DCC:DODECYL~~-~~COA'>DCC</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]] 2.15Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3whc\|3whc]], [[1vi0\|1vi0]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [https://pdbe.org/3whb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [https://www.ebi.ac.uk/pdbsum/3whb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb 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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [https://pdbe.org/3whb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [https://www.ebi.ac.uk/pdbsum/3whb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FADR_BACSU FADR_BACSU]] Transcriptional regulator in fatty acid degradation. Represses transcription of genes required for fatty acid transport and beta-oxidation, including acdA, fadA, fadB, fadE, fadF, fadG, fadH, fadM, fadN, lcfA and lcfB. Binding of FadR to DNA is specifically inhibited by long chain fatty acyl-CoA compounds of 14-20 carbon atoms in length.	+	[https://www.uniprot.org/uniprot/FADR_BACSU FADR_BACSU] Transcriptional regulator in fatty acid degradation. Represses transcription of genes required for fatty acid transport and beta-oxidation, including acdA, fadA, fadB, fadE, fadF, fadG, fadH, fadM, fadN, lcfA and lcfB. Binding of FadR to DNA is specifically inhibited by long chain fatty acyl-CoA compounds of 14-20 carbon atoms in length.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Bacillus subtilis FadR (FadRBs ), a member of the TetR family of bacterial transcriptional regulators, represses five fad operons including 15 genes, most of which are involved in beta-oxidation of fatty acids. FadRBs binds to the five FadRBs boxes in the promoter regions and the binding is specifically inhibited by long-chain (C14 -C20 ) acyl-CoAs, causing derepression of the fad operons. To elucidate the structural mechanism of this regulator, we have determined the crystal structures of FadRBs proteins prepared with and without stearoyl(C18 )-CoA. The crystal structure without adding any ligand molecules unexpectedly includes one small molecule, probably dodecyl(C12 )-CoA derived from the Escherichia coli host, in its homodimeric structure. Also, we successfully obtained the structure of the ligand-bound form of the FadRBs dimer by co-crystallization, in which two stearoyl-CoA molecules are accommodated, with the binding mode being essentially equivalent to that of dodecyl-CoA. Although the acyl-chain-binding cavity of FadRBs is mainly hydrophobic, a hydrophilic patch encompasses the C1-C10 carbons of the acyl chain. This accounts for the previous report that the DNA binding of FadRBs is specifically inhibited by the long-chain acyl-CoAs but not by the shorter ones. Structural comparison of the ligand-bound and unliganded subunits of FadRBs revealed three regions around residues 21-31, 61-76, and 106-119 that were substantially changed in response to the ligand binding, and particularly with respect to the movements of Leu108 and Arg109. Site-directed mutagenesis of these residues revealed that Arg109, but not Leu108, is a key residue for maintenance of the DNA-binding affinity of FadRBs . Proteins 2014. (c) 2013 Wiley Periodicals, Inc.	+
-		+
-	Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation.,Fujihashi M, Nakatani T, Hirooka K, Matsuoka H, Fujita Y, Miki K Proteins. 2013 Dec 20. doi: 10.1002/prot.24496. PMID:24356978<ref>PMID:24356978</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3whb" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fujihashi, M]]	+	[[Category: Fujihashi M]]
-	[[Category: Miki, K]]	+	[[Category: Miki K]]
-	[[Category: Nakatani, T]]	+	[[Category: Nakatani T]]
-	~~[[Category: Fatty acid degradation]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcriptional regulator~~]]	+

OCA at 05:36, 3 August 2022

OCA — Wed, 03 Aug 2022 05:36:30 GMT

←Older revision		Revision as of 05:36, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation==		==Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation==
-	<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='3whb' size='340' side='right'caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WHB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3whc\|3whc]], [[1vi0\|1vi0]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [~~http~~://pdbe.org/3whb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3whb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb 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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [https://pdbe.org/3whb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [https://www.ebi.ac.uk/pdbsum/3whb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FADR_BACSU FADR_BACSU]] Transcriptional regulator in fatty acid degradation. Represses transcription of genes required for fatty acid transport and beta-oxidation, including acdA, fadA, fadB, fadE, fadF, fadG, fadH, fadM, fadN, lcfA and lcfB. Binding of FadR to DNA is specifically inhibited by long chain fatty acyl-CoA compounds of 14-20 carbon atoms in length.	+	[[https://www.uniprot.org/uniprot/FADR_BACSU FADR_BACSU]] Transcriptional regulator in fatty acid degradation. Represses transcription of genes required for fatty acid transport and beta-oxidation, including acdA, fadA, fadB, fadE, fadF, fadG, fadH, fadM, fadN, lcfA and lcfB. Binding of FadR to DNA is specifically inhibited by long chain fatty acyl-CoA compounds of 14-20 carbon atoms in length.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bacsu]]		[[Category: Bacsu]]
		+	[[Category: Large Structures]]
	[[Category: Fujihashi, M]]		[[Category: Fujihashi, M]]
	[[Category: Miki, K]]		[[Category: Miki, K]]

OCA at 08:06, 22 November 2017

OCA — Wed, 22 Nov 2017 08:06:37 GMT

←Older revision		Revision as of 08:06, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [http://pdbe.org/3whb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [http://www.ebi.ac.uk/pdbsum/3whb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb 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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [http://pdbe.org/3whb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [http://www.ebi.ac.uk/pdbsum/3whb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Fujihashi, M]]		[[Category: Fujihashi, M]]
	[[Category: Miki, K]]		[[Category: Miki, K]]

OCA at 07:31, 9 March 2017

OCA — Thu, 09 Mar 2017 07:31:28 GMT

←Older revision		Revision as of 07:31, 9 March 2017
Line 3:		Line 3:
	<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [http://pdbe.org/3whb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [http://www.ebi.ac.uk/pdbsum/3whb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb 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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [http://pdbe.org/3whb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [http://www.ebi.ac.uk/pdbsum/3whb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb ProSAT]</span></td></tr>
	</table>		</table>
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacsu]]
	[[Category: Fujihashi, M]]		[[Category: Fujihashi, M]]
	[[Category: Miki, K]]		[[Category: Miki, K]]

OCA at 18:28, 4 August 2016

OCA — Thu, 04 Aug 2016 18:28:09 GMT

←Older revision		Revision as of 18:28, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation==		==Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation==
	<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [http://www.ebi.ac.uk/pdbsum/3whb 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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [http://pdbe.org/3whb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [http://www.ebi.ac.uk/pdbsum/3whb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3whb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3whb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:12, 24 December 2014

OCA — Wed, 24 Dec 2014 18:12:25 GMT

←Older revision		Revision as of 18:12, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3whb\| PDB=3whb \| SCENE= }}~~	+	==Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation==
-	===Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation===	+	<StructureSection load='3whb' size='340' side='right' caption='[[3whb]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24356978}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3whb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WHB FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCC:DODECYL-COA'>DCC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3whc\|3whc]], [[1vi0\|1vi0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fadR, ysiA, BSU28550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=3whb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3whb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3whb RCSB], [http://www.ebi.ac.uk/pdbsum/3whb PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/FADR_BACSU FADR_BACSU]] Transcriptional regulator in fatty acid degradation. Represses transcription of genes required for fatty acid transport and beta-oxidation, including acdA, fadA, fadB, fadE, fadF, fadG, fadH, fadM, fadN, lcfA and lcfB. Binding of FadR to DNA is specifically inhibited by long chain fatty acyl-CoA compounds of 14-20 carbon atoms in length.		[[http://www.uniprot.org/uniprot/FADR_BACSU FADR_BACSU]] Transcriptional regulator in fatty acid degradation. Represses transcription of genes required for fatty acid transport and beta-oxidation, including acdA, fadA, fadB, fadE, fadF, fadG, fadH, fadM, fadN, lcfA and lcfB. Binding of FadR to DNA is specifically inhibited by long chain fatty acyl-CoA compounds of 14-20 carbon atoms in length.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacillus subtilis FadR (FadRBs ), a member of the TetR family of bacterial transcriptional regulators, represses five fad operons including 15 genes, most of which are involved in beta-oxidation of fatty acids. FadRBs binds to the five FadRBs boxes in the promoter regions and the binding is specifically inhibited by long-chain (C14 -C20 ) acyl-CoAs, causing derepression of the fad operons. To elucidate the structural mechanism of this regulator, we have determined the crystal structures of FadRBs proteins prepared with and without stearoyl(C18 )-CoA. The crystal structure without adding any ligand molecules unexpectedly includes one small molecule, probably dodecyl(C12 )-CoA derived from the Escherichia coli host, in its homodimeric structure. Also, we successfully obtained the structure of the ligand-bound form of the FadRBs dimer by co-crystallization, in which two stearoyl-CoA molecules are accommodated, with the binding mode being essentially equivalent to that of dodecyl-CoA. Although the acyl-chain-binding cavity of FadRBs is mainly hydrophobic, a hydrophilic patch encompasses the C1-C10 carbons of the acyl chain. This accounts for the previous report that the DNA binding of FadRBs is specifically inhibited by the long-chain acyl-CoAs but not by the shorter ones. Structural comparison of the ligand-bound and unliganded subunits of FadRBs revealed three regions around residues 21-31, 61-76, and 106-119 that were substantially changed in response to the ligand binding, and particularly with respect to the movements of Leu108 and Arg109. Site-directed mutagenesis of these residues revealed that Arg109, but not Leu108, is a key residue for maintenance of the DNA-binding affinity of FadRBs . Proteins 2014. (c) 2013 Wiley Periodicals, Inc.

-	~~==About this Structure==~~	+	Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation.,Fujihashi M, Nakatani T, Hirooka K, Matsuoka H, Fujita Y, Miki K Proteins. 2013 Dec 20. doi: 10.1002/prot.24496. PMID:24356978<ref>PMID:24356978</ref>
-	~~[[3whb]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3WHB OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024356978</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Fujihashi, M.]]	+	== References ==
-	[[Category: Miki, K.]]	+	<references/>
-	[[Category: Nakatani, T.]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacsu]]
		+	[[Category: Fujihashi, M]]
		+	[[Category: Miki, K]]
		+	[[Category: Nakatani, T]]
	[[Category: Fatty acid degradation]]		[[Category: Fatty acid degradation]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcriptional regulator]]		[[Category: Transcriptional regulator]]

OCA at 08:42, 19 March 2014

OCA — Wed, 19 Mar 2014 08:42:04 GMT

←Older revision		Revision as of 08:42, 19 March 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3whb\| PDB=3whb \| SCENE= }}
		+	===Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation===
		+	{{ABSTRACT_PUBMED_24356978}}

-	~~The entry 3whb~~ is ~~ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/FADR_BACSU FADR_BACSU]] Transcriptional regulator in fatty acid degradation. Represses transcription of genes required for fatty acid transport and beta-oxidation, including acdA, fadA, fadB, fadE, fadF, fadG, fadH, fadM, fadN, lcfA and lcfB. Binding of FadR to DNA is specifically inhibited by long chain fatty acyl-CoA compounds of 14-20 carbon atoms in length.

-	~~Authors~~: ~~Fujihashi, M~~.~~, Nakatani, T~~.~~, Miki, K~~.	+	==About this Structure==
		+	[[3whb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WHB OCA].

-	~~Description~~: ~~Crystal structure of FadR from Bacillus subtilis~~, ~~a transcriptional regulator involved in the regulation of fatty~~ acid degradation	+	==Reference==
		+	<ref group="xtra">PMID:024356978</ref><references group="xtra"/><references/>
		+	[[Category: Fujihashi, M.]]
		+	[[Category: Miki, K.]]
		+	[[Category: Nakatani, T.]]
		+	[[Category: Fatty acid degradation]]
		+	[[Category: Transcription]]
		+	[[Category: Transcriptional regulator]]

OCA at 07:04, 16 October 2013

OCA — Wed, 16 Oct 2013 07:04:34 GMT

←Older revision		Revision as of 07:04, 16 October 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3whb is ON HOLD	+	The entry 3whb is ON HOLD until Paper Publication

	Authors: Fujihashi, M., Nakatani, T., Miki, K.		Authors: Fujihashi, M., Nakatani, T., Miki, K.

	Description: Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation		Description: Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation

OCA: Protected "3whb" [edit=sysop:move=sysop]

OCA — Wed, 28 Aug 2013 06:17:43 GMT

Protected "3whb" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:17, 28 August 2013

OCA: New page: '''Unreleased structure''' The entry 3whb is ON HOLD Authors: Fujihashi, M., Nakatani, T., Miki, K. Description: Crystal structure of FadR from Bacillus subtilis, a transcriptional reg...

OCA — Wed, 28 Aug 2013 06:17:42 GMT

New page: '''Unreleased structure''' The entry 3whb is ON HOLD Authors: Fujihashi, M., Nakatani, T., Miki, K. Description: Crystal structure of FadR from Bacillus subtilis, a transcriptional reg...

New page

'''Unreleased structure'''

The entry 3whb is ON HOLD

Authors: Fujihashi, M., Nakatani, T., Miki, K.

Description: Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation