3t22 - Revision history

OCA at 13:15, 14 March 2024

OCA — Thu, 14 Mar 2024 13:15:09 GMT

←Older revision		Revision as of 13:15, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3t22' size='340' side='right'caption='[[3t22]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3t22' size='340' side='right'caption='[[3t22]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t22]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_33277 Atcc 33277~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T22 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t22]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T22 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3ho7\|3ho7]]</div></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]] 2.2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">oxyR ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=837 ATCC 33277])~~</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=3t22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t22 OCA], [https://pdbe.org/3t22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t22 RCSB], [https://www.ebi.ac.uk/pdbsum/3t22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t22 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=3t22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t22 OCA], [https://pdbe.org/3t22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t22 RCSB], [https://www.ebi.ac.uk/pdbsum/3t22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t22 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q20K61_PORGN Q20K61_PORGN]
-	OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR-DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.	+
-		+
-	Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis.,Svintradze DV, Peterson DL, Collazo-Santiago EA, Lewis JP, Wright HT Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):~~2091-103. doi:, 10.1107~~/~~S0907444913019471. Epub 2013 Sep 20. PMID:24100327<ref>PMID:24100327<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3t22" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]		*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 33277]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lewis, J P~~]]	+	[[Category: Porphyromonas gingivalis]]
-	[[Category: ~~Svintradze, D V~~]]	+	[[Category: Lewis JP]]
-	[[Category: ~~Wright, H T~~]]	+	[[Category: Svintradze DV]]
-	[[Category: ~~Beta-alpha-barrel]]~~	+	[[Category: Wright HT]]
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 16:39, 6 July 2022

OCA — Wed, 06 Jul 2022 16:39:49 GMT

←Older revision		Revision as of 16:39, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of OxyR mutant from Porphyromonas gingivalis==		==Crystal structure of OxyR mutant from Porphyromonas gingivalis==
-	<StructureSection load='3t22' size='340' side='right' caption='[[3t22]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='3t22' size='340' side='right'caption='[[3t22]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t22]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_33277 Atcc 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3T22 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t22]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33277 Atcc 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T22 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ho7\|3ho7]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ho7\|3ho7]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxyR ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxyR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])</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=3t22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t22 OCA], [~~http~~://pdbe.org/3t22 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3t22 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3t22 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3t22 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=3t22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t22 OCA], [https://pdbe.org/3t22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t22 RCSB], [https://www.ebi.ac.uk/pdbsum/3t22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t22 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Transcriptional activator\|Transcriptional activator]]	+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 33277]]		[[Category: Atcc 33277]]
		+	[[Category: Large Structures]]
	[[Category: Lewis, J P]]		[[Category: Lewis, J P]]
	[[Category: Svintradze, D V]]		[[Category: Svintradze, D V]]

OCA at 21:17, 5 August 2016

OCA — Fri, 05 Aug 2016 21:17:48 GMT

←Older revision		Revision as of 21:17, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of OxyR mutant from Porphyromonas gingivalis==		==Crystal structure of OxyR mutant from Porphyromonas gingivalis==
	<StructureSection load='3t22' size='340' side='right' caption='[[3t22]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3t22' size='340' side='right' caption='[[3t22]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ho7\|3ho7]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ho7\|3ho7]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxyR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxyR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])</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=3t22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t22 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t22 RCSB], [http://www.ebi.ac.uk/pdbsum/3t22 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=3t22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t22 OCA], [http://pdbe.org/3t22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t22 RCSB], [http://www.ebi.ac.uk/pdbsum/3t22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t22 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3t22" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 16:36, 21 December 2014

OCA — Sun, 21 Dec 2014 16:36:38 GMT

←Older revision		Revision as of 16:36, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3t22\| PDB=3t22 \| SCENE= }}~~	+	==Crystal structure of OxyR mutant from Porphyromonas gingivalis==
-	===Crystal structure of OxyR mutant from Porphyromonas gingivalis===	+	<StructureSection load='3t22' size='340' side='right' caption='[[3t22]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24100327}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3t22]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33277 Atcc 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T22 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ho7\|3ho7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxyR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])</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=3t22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t22 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t22 RCSB], [http://www.ebi.ac.uk/pdbsum/3t22 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR-DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.

-	~~==About this Structure==~~	+	Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis.,Svintradze DV, Peterson DL, Collazo-Santiago EA, Lewis JP, Wright HT Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):2091-103. doi:, 10.1107/S0907444913019471. Epub 2013 Sep 20. PMID:24100327<ref>PMID:24100327</ref>
-	~~[[3t22]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Atcc_33277 Atcc 33277]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3T22 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:024100327</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Transcriptional activator\|Transcriptional activator]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Atcc 33277]]		[[Category: Atcc 33277]]
-	[[Category: Lewis, J P.]]	+	[[Category: Lewis, J P]]
-	[[Category: Svintradze, D V.]]	+	[[Category: Svintradze, D V]]
-	[[Category: Wright, H T.]]	+	[[Category: Wright, H T]]
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]

OCA at 08:23, 27 November 2013

OCA — Wed, 27 Nov 2013 08:23:36 GMT

←Older revision		Revision as of 08:23, 27 November 2013
Line 1:		Line 1:
	{{STRUCTURE_3t22\| PDB=3t22 \| SCENE= }}		{{STRUCTURE_3t22\| PDB=3t22 \| SCENE= }}
	===Crystal structure of OxyR mutant from Porphyromonas gingivalis===		===Crystal structure of OxyR mutant from Porphyromonas gingivalis===
		+	{{ABSTRACT_PUBMED_24100327}}

	==About this Structure==		==About this Structure==
-	[[3t22]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Porphyromonas_gingivalis Porphyromonas gingivalis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA].	+	[[3t22]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33277 Atcc 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA].
-	[[Category: ~~Porphyromonas gingivalis~~]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:024100327</ref><references group="xtra"/><references/>
		+	[[Category: Atcc 33277]]
	[[Category: Lewis, J P.]]		[[Category: Lewis, J P.]]
	[[Category: Svintradze, D V.]]		[[Category: Svintradze, D V.]]

OCA at 20:29, 17 April 2013

OCA — Wed, 17 Apr 2013 20:29:53 GMT

←Older revision		Revision as of 20:29, 17 April 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3t22\| PDB=3t22 \| SCENE= }}
		+	===Crystal structure of OxyR mutant from Porphyromonas gingivalis===

-	~~The entry~~ 3t22 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3t22]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T22 OCA].
-	~~Authors~~: Svintradze, D.V., Wright, H.T.~~, Lewis, J.P.~~	+	[[Category: Porphyromonas gingivalis]]
-		+	[[Category: Lewis, J P.]]
-	~~Description~~: ~~Crystal structure of OxyR mutant from Porphyromonas gingivalis~~	+	[[Category: Svintradze, D V.]]
		+	[[Category: Wright, H T.]]
		+	[[Category: Beta-alpha-barrel]]
		+	[[Category: Dna-binding]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Transcription regulator]]

OCA at 05:33, 10 August 2011

OCA — Wed, 10 Aug 2011 05:33:15 GMT

←Older revision		Revision as of 05:33, 10 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3t22 is ON HOLD	+	The entry 3t22 is ON HOLD until Paper Publication

	Authors: Svintradze, D.V., Wright, H.T., Lewis, J.P.		Authors: Svintradze, D.V., Wright, H.T., Lewis, J.P.

	Description: Crystal structure of OxyR mutant from Porphyromonas gingivalis		Description: Crystal structure of OxyR mutant from Porphyromonas gingivalis

OCA: Protected "3t22" [edit=sysop:move=sysop]

OCA — Wed, 03 Aug 2011 08:23:50 GMT

Protected "3t22" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:23, 3 August 2011

OCA: New page: '''Unreleased structure''' The entry 3t22 is ON HOLD Authors: Svintradze, D.V., Wright, H.T., Lewis, J.P. Description: Crystal structure of OxyR mutant from Porphyromonas gingivalis

OCA — Wed, 03 Aug 2011 08:23:49 GMT

New page: '''Unreleased structure''' The entry 3t22 is ON HOLD Authors: Svintradze, D.V., Wright, H.T., Lewis, J.P. Description: Crystal structure of OxyR mutant from Porphyromonas gingivalis

New page

'''Unreleased structure'''

The entry 3t22 is ON HOLD

Authors: Svintradze, D.V., Wright, H.T., Lewis, J.P.

Description: Crystal structure of OxyR mutant from Porphyromonas gingivalis