5deq - Revision history

OCA at 10:32, 21 June 2023

OCA — Wed, 21 Jun 2023 10:32:33 GMT

←Older revision		Revision as of 10:32, 21 June 2023
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	<StructureSection load='5deq' size='340' side='right'caption='[[5deq]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5deq' size='340' side='right'caption='[[5deq]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5deq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DEQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5deq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DEQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=5deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5deq OCA], [https://pdbe.org/5deq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5deq RCSB], [https://www.ebi.ac.uk/pdbsum/5deq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5deq ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ddg\|5ddg]], [[5dd4\|5dd4]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_0354 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])~~</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=5deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5deq OCA], [~~http~~://pdbe.org/5deq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5deq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5deq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5deq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8AAV8_BACTN Q8AAV8_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5deq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5deq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bactn~~]]	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang, C]]	+	[[Category: Chang C]]
-	[[Category: Joachimiak, A]]	+	[[Category: Joachimiak A]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Rodionov D]]
-	[[Category: Rodionov, D]]	+	[[Category: Tesar C]]
-	[[Category: Tesar, C]]	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 08:01, 8 April 2020

OCA — Wed, 08 Apr 2020 08:01:10 GMT

←Older revision		Revision as of 08:01, 8 April 2020
Line 1:		Line 1:
		+
	==Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with L-arabinose==		==Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with L-arabinose==
-	<StructureSection load='5deq' size='340' side='right' caption='[[5deq]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5deq' size='340' side='right'caption='[[5deq]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5deq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5deq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DEQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ddg\|5ddg]], [[5dd4\|5dd4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ddg\|5ddg]], [[5dd4\|5dd4]]</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=5deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5deq OCA], [http://pdbe.org/5deq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5deq RCSB], [http://www.ebi.ac.uk/pdbsum/5deq PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_0354 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</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=5deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5deq OCA], [http://pdbe.org/5deq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5deq RCSB], [http://www.ebi.ac.uk/pdbsum/5deq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5deq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bactn]]
		+	[[Category: Large Structures]]
	[[Category: Chang, C]]		[[Category: Chang, C]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 05:24, 22 October 2015

OCA — Thu, 22 Oct 2015 05:24:37 GMT

←Older revision		Revision as of 05:24, 22 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with L-arabinose==
		+	<StructureSection load='5deq' size='340' side='right' caption='[[5deq]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5deq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DEQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ddg\|5ddg]], [[5dd4\|5dd4]]</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=5deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5deq OCA], [http://pdbe.org/5deq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5deq RCSB], [http://www.ebi.ac.uk/pdbsum/5deq PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.

-	~~The entry 5deq is ON HOLD~~	+	A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.,Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A Nucleic Acids Res. 2015 Oct 4. pii: gkv1005. PMID:26438537<ref>PMID:26438537</ref>

-	~~Authors: Chang~~, C.~~, Tesar, C~~.~~, Rodionov, D~~.~~, Joachimiak, A., Midwest Center for Structural Genomics (MCSG)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with L-arabinose~~	+	<div class="pdbe-citations 5deq" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chang, C]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]
		+	[[Category: Structural genomic]]
		+	[[Category: Rodionov, D]]
	[[Category: Tesar, C]]		[[Category: Tesar, C]]
-	[[Category: ~~Midwest Center For Structural Genomics (~~Mcsg)]]	+	[[Category: Mcsg]]
-	[[Category: ~~Rodionov, D~~]]	+	[[Category: Psi-biology]]
-	[[Category: ~~Chang, C~~]]	+	[[Category: Transcription regulator]]

OCA at 12:55, 30 September 2015

OCA — Wed, 30 Sep 2015 12:55:50 GMT

←Older revision		Revision as of 12:55, 30 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5deq is ON HOLD ~~until sometime in the future~~	+	The entry 5deq is ON HOLD

	Authors: Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)		Authors: Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

OCA at 10:05, 9 September 2015

OCA — Wed, 09 Sep 2015 10:05:51 GMT

←Older revision		Revision as of 10:05, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5deq is ON HOLD	+	The entry 5deq is ON HOLD until sometime in the future

	Authors: Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)		Authors: Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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

OCA — Wed, 02 Sep 2015 11:33:29 GMT

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

←Older revision

Revision as of 11:33, 2 September 2015

OCA: New page: '''Unreleased structure''' The entry 5deq is ON HOLD Authors: Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG) Description: Crystal str...

OCA — Wed, 02 Sep 2015 11:33:28 GMT

New page: '''Unreleased structure''' The entry 5deq is ON HOLD Authors: Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG) Description: Crystal str...

New page

'''Unreleased structure'''

The entry 5deq is ON HOLD

Authors: Chang, C., Tesar, C., Rodionov, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Description: Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with L-arabinose
[[Category: Unreleased Structures]]
[[Category: Joachimiak, A]]
[[Category: Tesar, C]]
[[Category: Midwest Center For Structural Genomics (Mcsg)]]
[[Category: Rodionov, D]]
[[Category: Chang, C]]