5k7f - Revision history

OCA at 10:42, 27 September 2023

2023-09-27T10:42:25Z

←Older revision		Revision as of 10:42, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5k7f' size='340' side='right'caption='[[5k7f]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5k7f' size='340' side='right'caption='[[5k7f]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k7f]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myxxd Myxxd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K7F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k7f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myxococcus_xanthus_DK_1622 Myxococcus xanthus DK 1622]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K7F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MXAN_4263 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=246197 MYXXD])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5k7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7f OCA], [~~http~~://pdbe.org/5k7f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k7f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k7f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7f 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=5k7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7f OCA], [https://pdbe.org/5k7f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k7f RCSB], [https://www.ebi.ac.uk/pdbsum/5k7f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7f ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q1D4I5_MYXXD Q1D4I5_MYXXD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5k7f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k7f" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myxxd~~]]	+	[[Category: Myxococcus xanthus DK 1622]]
-	[[Category: Blankenfeldt, W]]	+	[[Category: Blankenfeldt W]]
-	[[Category: Bock, T]]	+	[[Category: Bock T]]
-	[[Category: Mueller, R]]	+	[[Category: Mueller R]]
-	[[Category: Volz, C]]	+	[[Category: Volz C]]
-	~~[[Category: Isovalerate]]~~	+
-	~~[[Category: Regulation]]~~	+
-	~~[[Category: Tetr like regulator]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 09:24, 1 July 2020

2020-07-01T09:24:36Z

←Older revision		Revision as of 09:24, 1 July 2020
Line 1:		Line 1:

	==Crystal structure of apo AibR==		==Crystal structure of apo AibR==
-	<StructureSection load='5k7f' size='340' side='right' caption='[[5k7f]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5k7f' size='340' side='right'caption='[[5k7f]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k7f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7F OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K7F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myxxd Myxxd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K7F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></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=5k7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7f OCA], [http://pdbe.org/5k7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k7f RCSB], [http://www.ebi.ac.uk/pdbsum/5k7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7f ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MXAN_4263 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246197 MYXXD])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7f OCA], [http://pdbe.org/5k7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k7f RCSB], [http://www.ebi.ac.uk/pdbsum/5k7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7f ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Myxxd]]
	[[Category: Blankenfeldt, W]]		[[Category: Blankenfeldt, W]]
	[[Category: Bock, T]]		[[Category: Bock, T]]

OCA at 21:30, 22 December 2016

2016-12-22T21:30:03Z

←Older revision		Revision as of 21:30, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k7f is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of apo AibR==
		+	<StructureSection load='5k7f' size='340' side='right' caption='[[5k7f]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k7f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K7F FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></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=5k7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7f OCA], [http://pdbe.org/5k7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k7f RCSB], [http://www.ebi.ac.uk/pdbsum/5k7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7f ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isovaleryl coenzyme A (IV-CoA) is an important building block of iso-fatty acids. In myxobacteria, IV-CoA is essential for the formation of signaling molecules involved in fruiting body formation. Leucine degradation is the common source of IV-CoA, but a second, de novo biosynthetic route to IV-CoA termed AIB (alternative IV-CoA biosynthesis) was recently discovered in M. xanthus The AIB-operon contains the TetR-like transcriptional regulator AibR, which we characterize in this study. We demonstrate that IV-CoA binds AibR with micromolar affinity and show by gelshift experiments that AibR interacts with the promoter region of the AIB-operon once IV-CoA is present. We identify an 18-bp near-perfect palindromic repeat as containing the AibR operator and provide evidence that AibR also controls an additional genomic locus coding for a putative acetyl-CoA acetyltransferase. To elucidate atomic details, we determined crystal structures of AibR in the apo, the IV-CoA- and the IV-CoA-DNA-bound state to 1.7 A, 2.35 A and 2.92 A, respectively. IV-CoA induces partial unfolding of an alpha-helix, which allows sequence-specific interactions between AibR and its operator. This study provides insights into AibR-mediated regulation and shows that AibR functions in an unusual TetR-like manner by blocking transcription not in the ligand-free but in the effector-bound state.

-	~~Authors~~:	+	The AibR-isovaleryl coenzyme A regulator and its DNA binding site - a model for the regulation of alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus.,Bock T, Volz C, Hering V, Scrima A, Muller R, Blankenfeldt W Nucleic Acids Res. 2016 Dec 9. pii: gkw1238. PMID:27940564<ref>PMID:27940564</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k7f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Blankenfeldt, W]]
		+	[[Category: Bock, T]]
		+	[[Category: Mueller, R]]
		+	[[Category: Volz, C]]
		+	[[Category: Isovalerate]]
		+	[[Category: Regulation]]
		+	[[Category: Tetr like regulator]]
		+	[[Category: Transcription]]

OCA: Protected "5k7f" [edit=sysop:move=sysop]

2016-06-01T14:25:25Z

Protected "5k7f" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:25, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k7f is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2016-06-01T14:25:23Z

New page: '''Unreleased structure''' The entry 5k7f is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k7f is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]