7acm - Revision history

OCA at 12:07, 1 February 2024

OCA — Thu, 01 Feb 2024 12:07:16 GMT

←Older revision		Revision as of 12:07, 1 February 2024
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	<StructureSection load='7acm' size='340' side='right'caption='[[7acm]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='7acm' size='340' side='right'caption='[[7acm]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7acm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ACM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ACM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7acm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ACM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ACM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</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]] 1.763Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rcdA, ybjK, b0846, JW5114 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</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=7acm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7acm OCA], [https://pdbe.org/7acm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7acm RCSB], [https://www.ebi.ac.uk/pdbsum/7acm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7acm 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=7acm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7acm OCA], [https://pdbe.org/7acm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7acm RCSB], [https://www.ebi.ac.uk/pdbsum/7acm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7acm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RCDA_ECOLI RCDA_ECOLI]] Regulates the expression of a number of genes involved in biofilm formation and stress response. Target genes include six stress-response transcriptional regulators: csgD, which is a master regulator of biofilm formation, appY, sxy, ycgF, fimB and rcdA itself. This indicates that a large number of genes must be regulated indirectly via these transcriptional regulators. Acts by binding to the upstream region of its target genes.<ref>PMID:23233451</ref>	+	[https://www.uniprot.org/uniprot/RCDA_ECOLI RCDA_ECOLI] Regulates the expression of a number of genes involved in biofilm formation and stress response. Target genes include six stress-response transcriptional regulators: csgD, which is a master regulator of biofilm formation, appY, sxy, ycgF, fimB and rcdA itself. This indicates that a large number of genes must be regulated indirectly via these transcriptional regulators. Acts by binding to the upstream region of its target genes.<ref>PMID:23233451</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7acm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7acm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RcdA\|RcdA]]
		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cociurovscaia, A]]	+	[[Category: Cociurovscaia A]]
-	[[Category: Pietrzyk-Brzezinska~~, A J]]~~	+	[[Category: Pietrzyk-Brzezinska AJ]]
-	~~[[Category: Dna-binding protein]]~~	+
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Hth motif]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 08:58, 29 September 2021

OCA — Wed, 29 Sep 2021 08:58:28 GMT

←Older revision		Revision as of 08:58, 29 September 2021
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	==Crystal structure of E. coli HTH-type transcriptional regulator RcdA in complex with TMAO at 1.76 A resolution==		==Crystal structure of E. coli HTH-type transcriptional regulator RcdA in complex with TMAO at 1.76 A resolution==
-	<StructureSection load='7acm' size='340' side='right'caption='[[7acm]]' scene=''>	+	<StructureSection load='7acm' size='340' side='right'caption='[[7acm]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ACM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ACM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7acm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ACM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ACM FirstGlance]. <br>
-	</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=7acm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7acm OCA], [https://pdbe.org/7acm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7acm RCSB], [https://www.ebi.ac.uk/pdbsum/7acm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7acm ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rcdA, ybjK, b0846, JW5114 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=7acm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7acm OCA], [https://pdbe.org/7acm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7acm RCSB], [https://www.ebi.ac.uk/pdbsum/7acm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7acm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/RCDA_ECOLI RCDA_ECOLI]] Regulates the expression of a number of genes involved in biofilm formation and stress response. Target genes include six stress-response transcriptional regulators: csgD, which is a master regulator of biofilm formation, appY, sxy, ycgF, fimB and rcdA itself. This indicates that a large number of genes must be regulated indirectly via these transcriptional regulators. Acts by binding to the upstream region of its target genes.<ref>PMID:23233451</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RcdA is a helix-turn-helix (HTH) transcriptional regulator belonging to the TetR family. The protein regulates the transcription of curlin subunit gene D, the master regulator of biofilm formation. Moreover, it was predicted that it might be involved in the regulation of up to 27 different genes. However, an effector of RcdA and the environmental conditions which trigger RcdA action remain unknown. Herein, we report the first crystal structures of RcdA in complexes with ligands, trimethylamine N-oxide (TMAO) and tris(hydroxymethyl)aminomethane (Tris), which might serve as RcdA effectors. Based on these structures, the ligand-binding pocket of RcdA was characterized in detail. The conservation of the amino acid residues forming the ligand-binding cavity was analyzed and the comprehensive search for RcdA structural homologs was performed. This analysis indicated that RcdA is structurally similar to multidrug-binding TetR family members, however, its ligand-binding cavity differs significantly from the pockets of its structural homologs. The interaction of RcdA with TMAO and Tris indicates that the protein might be involved in alkaline stress response.
		+
		+	Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands.,Pietrzyk-Brzezinska AJ, Cociurovscaia A Proteins. 2021 Jul 20. doi: 10.1002/prot.26183. PMID:34288132<ref>PMID:34288132</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7acm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cociurovscaia A]]	+	[[Category: Cociurovscaia, A]]
-	[[Category: Pietrzyk-Brzezinska AJ]]	+	[[Category: Pietrzyk-Brzezinska, A J]]
		+	[[Category: Dna-binding protein]]
		+	[[Category: Gene regulation]]
		+	[[Category: Hth motif]]
		+	[[Category: Transcription factor]]

OCA at 06:06, 18 August 2021

OCA — Wed, 18 Aug 2021 06:06:59 GMT

←Older revision		Revision as of 06:06, 18 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7acm ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of E. coli HTH-type transcriptional regulator RcdA in complex with TMAO at 1.76 A resolution==
-		+	<StructureSection load='7acm' size='340' side='right'caption='[[7acm]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ACM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ACM FirstGlance]. <br>
-	~~Description~~:	+	</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=7acm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7acm OCA], [https://pdbe.org/7acm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7acm RCSB], [https://www.ebi.ac.uk/pdbsum/7acm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7acm ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cociurovscaia A]]
		+	[[Category: Pietrzyk-Brzezinska AJ]]

OCA at 08:41, 23 September 2020

OCA — Wed, 23 Sep 2020 08:41:25 GMT

←Older revision		Revision as of 08:41, 23 September 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7acm is ON HOLD	+	The entry 7acm is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7acm" [edit=sysop:move=sysop]

OCA — Wed, 16 Sep 2020 06:45:38 GMT

Protected "7acm" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:45, 16 September 2020

OCA: New page: '''Unreleased structure''' The entry 7acm is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Sep 2020 06:45:37 GMT

New page: '''Unreleased structure''' The entry 7acm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7acm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]