4tv7 - Revision history

OCA at 10:57, 15 March 2023

OCA — Wed, 15 Mar 2023 10:57:01 GMT

←Older revision		Revision as of 10:57, 15 March 2023
Line 3:		Line 3:
	<StructureSection load='4tv7' size='340' side='right'caption='[[4tv7]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='4tv7' size='340' side='right'caption='[[4tv7]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tv7]] is a 4 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=4TV7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4TV7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tv7]] is a 4 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=4TV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TV7 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gabR, ycnF, BSU03890 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=4tv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tv7 OCA], [https://pdbe.org/4tv7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tv7 RCSB], [https://www.ebi.ac.uk/pdbsum/4tv7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tv7 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=4tv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tv7 OCA], [~~http~~://pdbe.org/4tv7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4tv7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4tv7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4tv7 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GABR_BACSU GABR_BACSU]] Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.<ref>PMID:12123465</ref> <ref>PMID:15223311</ref>	+	[https://www.uniprot.org/uniprot/GABR_BACSU GABR_BACSU] Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.<ref>PMID:12123465</ref> <ref>PMID:15223311</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 4tv7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4tv7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Goto, M]]	+	[[Category: Goto M]]
-	[[Category: Okuda, K]]	+	[[Category: Okuda K]]
-	[[Category: Yoshimura, T]]	+	[[Category: Yoshimura T]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcriptional regulator~~]]	+

OCA at 13:55, 10 May 2019

OCA — Fri, 10 May 2019 13:55:03 GMT

←Older revision		Revision as of 13:55, 10 May 2019
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	==Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution==		==Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution==
-	<StructureSection load='4tv7' size='340' side='right' caption='[[4tv7]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='4tv7' size='340' side='right'caption='[[4tv7]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tv7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TV7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tv7]] is a 4 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=4TV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TV7 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gabR, ycnF, BSU03890 ([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=4tv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tv7 OCA], [http://pdbe.org/4tv7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tv7 RCSB], [http://www.ebi.ac.uk/pdbsum/4tv7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tv7 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=4tv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tv7 OCA], [http://pdbe.org/4tv7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tv7 RCSB], [http://www.ebi.ac.uk/pdbsum/4tv7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tv7 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
		+	[[Category: Large Structures]]
	[[Category: Goto, M]]		[[Category: Goto, M]]
	[[Category: Okuda, K]]		[[Category: Okuda, K]]

OCA at 13:17, 15 March 2017

OCA — Wed, 15 Mar 2017 13:17:55 GMT

←Older revision		Revision as of 13:17, 15 March 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GABR_BACSU GABR_BACSU]] Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.<ref>PMID:12123465</ref> <ref>PMID:15223311</ref>		[[http://www.uniprot.org/uniprot/GABR_BACSU GABR_BACSU]] Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.<ref>PMID:12123465</ref> <ref>PMID:15223311</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	MocR/GabR family proteins are widely distributed prokaryotic transcriptional regulators containing pyridoxal 5'-phosphate (PLP), a coenzyme form of vitamin B6. The Bacillus subtilis GabR, probably the most extensively studied MocR/GabR family protein, consists of an N-terminal DNA-binding domain and a PLP-binding C-terminal domain that has a structure homologous to aminotransferases. GabR suppresses transcription of gabR and activates transcription of gabT and gabD, which encode gamma-aminobutyrate (GAlphaBetaAlpha) aminotransferase and succinate semialdehyde dehydrogenase, respectively, in the presence of PLP and GABA. In this study, we examined the mechanism underlying GabR-mediated gabTD transcription with spectroscopic, crystallographic and thermodynamic studies, focusing on the function of the aminotransferase domain. Spectroscopic studies revealed that GABA forms an external aldimine with the PLP in the aminotransferase domain. Isothermal calorimetry demonstrated that two GabR molecules bind to the 51-bp DNA fragment that contains the GabR-binding region. GABA minimally affected DeltaG(binding) upon binding of GabR to the DNA fragment but greatly affected the contributions of DeltaH and DeltaS to DeltaG(binding). GABA forms an external aldimine with PLP and causes a conformational change in the aminotransferase domain, and this change likely rearranges GabR binding to the promoter and thus activates gabTD transcription.
		+
		+	Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator.,Okuda K, Kato S, Ito T, Shiraki S, Kawase Y, Goto M, Kawashima S, Hemmi H, Fukada H, Yoshimura T Mol Microbiol. 2015 Jan;95(2):245-57. doi: 10.1111/mmi.12861. Epub 2014 Dec 8. PMID:25388514<ref>PMID:25388514</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4tv7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:42, 4 August 2016

OCA — Thu, 04 Aug 2016 09:42:12 GMT

←Older revision		Revision as of 09:42, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution==		==Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution==
	<StructureSection load='4tv7' size='340' side='right' caption='[[4tv7]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='4tv7' size='340' side='right' caption='[[4tv7]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tv7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TV7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tv7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TV7 FirstGlance]. <br>
-	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-~~LYSINE(~~3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-~~YLMETHANE)~~'>LLP</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=4tv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tv7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tv7 RCSB], [http://www.ebi.ac.uk/pdbsum/4tv7 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=4tv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tv7 OCA], [http://pdbe.org/4tv7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tv7 RCSB], [http://www.ebi.ac.uk/pdbsum/4tv7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tv7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:27, 24 December 2014

OCA — Wed, 24 Dec 2014 08:27:19 GMT

←Older revision		Revision as of 08:27, 24 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution==
-		+	<StructureSection load='4tv7' size='340' side='right' caption='[[4tv7]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~The entry~~ 4tv7 is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4tv7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TV7 FirstGlance]. <br>
-	~~Authors~~: ~~Goto~~, M., ~~Okuda~~, K., Yoshimura, T.	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</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=4tv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tv7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tv7 RCSB], [http://www.ebi.ac.uk/pdbsum/4tv7 PDBsum]</span></td></tr>
-	~~Description~~: ~~Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution~~	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GABR_BACSU GABR_BACSU]] Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.<ref>PMID:12123465</ref> <ref>PMID:15223311</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Goto, M]]
		+	[[Category: Okuda, K]]
		+	[[Category: Yoshimura, T]]
		+	[[Category: Transcription]]
		+	[[Category: Transcriptional regulator]]

OCA at 06:58, 9 July 2014

OCA — Wed, 09 Jul 2014 06:58:20 GMT

←Older revision		Revision as of 06:58, 9 July 2014
Line 5:		Line 5:
	Authors: Goto, M., Okuda, K., Yoshimura, T.		Authors: Goto, M., Okuda, K., Yoshimura, T.

-	Description: Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution.	+	Description: Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution

OCA: Protected "4tv7" [edit=sysop:move=sysop]

OCA — Wed, 02 Jul 2014 07:35:40 GMT

Protected "4tv7" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:35, 2 July 2014

OCA: New page: '''Unreleased structure''' The entry 4tv7 is ON HOLD Authors: Goto, M., Okuda, K., Yoshimura, T. Description: Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution.

OCA — Wed, 02 Jul 2014 07:35:39 GMT

New page: '''Unreleased structure''' The entry 4tv7 is ON HOLD Authors: Goto, M., Okuda, K., Yoshimura, T. Description: Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution.

New page

'''Unreleased structure'''

The entry 4tv7 is ON HOLD

Authors: Goto, M., Okuda, K., Yoshimura, T.

Description: Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution.