2dtr - Revision history

OCA at 09:19, 14 February 2024

2024-02-14T09:19:06Z

← Older revision		Revision as of 09:19, 14 February 2024
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	<StructureSection load='2dtr' size='340' side='right'caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dtr' size='340' side='right'caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus~~ diphtheriae~~" kruse in flugge 1886~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTR FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">T (~~[https:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [https://pdbe.org/2dtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [https://www.ebi.ac.uk/pdbsum/2dtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtr 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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [https://pdbe.org/2dtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [https://www.ebi.ac.uk/pdbsum/2dtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.		[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dtr ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dtr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The crystal structure of diphtheria toxin repressor (DtxR) in complex with the corepressor Co2+ has been determined at 2.0 A resolution and in complex with Mn2+ at 2.2 A resolution. The structure of the flexible third domain could be determined at this high resolution. It appears to contain five antiparallel strands exhibiting a fold very similar to the SH3 domain. A superposition of 46 equivalent C alpha atoms of DtxR and alpha-spectrin SH3 resulted in an rms deviation of 3.0 A. The sequence identity is only 7%. This third domain of DtxR appears to have no interactions with the DNA binding domain nor with the metal binding domain of the repressor. Yet, flexibility in the region between the second and the third domain allows in principle significant conformational changes such as might occur upon DNA binding. The two metal binding sites in the second domain have been unraveled in considerable detail. Metal binding site 1 was well occupied in both the cobalt and manganese structures and showed a surprising sulfate ion as ligand. The sulfate was proven beyond doubt by the high peak at its position in a selenate versus sulfate difference Fourier. The presence of the intriguing sulfate ion at such a crucial position near the metal corepressor suggests the possibility that under physiological conditions phosphate may act as a "co-corepressor" for this class of metal-regulated DNA binding proteins in Corynebacteria, Mycobacteria, and related organisms. The second metal binding site is significantly different in these two DtxR structures. In the 2.0 A cobalt structure, the site is not occupied by a metal ion. In the 2.2 A manganese structure the site is well occupied, at approximately the same position as observed previously in cadmium DtxR. The ligands are Glu105, His106, the carbonyl oxygen of Cys102, and a water molecule. The reasons for differential occupancy of this site in different structures are intriguing and require further investigations.

	High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor.,Qiu X, Pohl E, Holmes RK, Hol WG Biochemistry. 1996 Sep 24;35(38):12292-302. PMID:8823163<ref>PMID:8823163</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2dtr" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]		*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ diphtheriae ~~kruse in flugge 1886~~]]		[[Category: Corynebacterium diphtheriae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hol~~, W G~~]]		[[Category: Hol WG]]
	[[Category: Pohl, E]]		[[Category: Pohl E]]
	[[Category: Qiu, X]]		[[Category: Qiu X]]
	~~[[Category: Dna-binding]]~~
	~~[[Category: Iron]]~~
	~~[[Category: Repressor]]~~
	~~[[Category: Transcription regulation~~]]

OCA at 11:37, 10 February 2021

2021-02-10T11:37:43Z

← Older revision		Revision as of 11:37, 10 February 2021
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	==STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR==		==STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR==
	<StructureSection load='2dtr' size='340' side='right' caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dtr' size='340' side='right'caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [~~http~~://pdbe.org/2dtr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dtr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtr 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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [https://pdbe.org/2dtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [https://www.ebi.ac.uk/pdbsum/2dtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.		[[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus diphtheriae kruse in flugge 1886]]		[[Category: Bacillus diphtheriae kruse in flugge 1886]]
			[[Category: Large Structures]]
	[[Category: Hol, W G]]		[[Category: Hol, W G]]
	[[Category: Pohl, E]]		[[Category: Pohl, E]]

OCA at 06:56, 6 June 2018

2018-06-06T06:56:30Z

← Older revision		Revision as of 06:56, 6 June 2018
Line 1:		Line 1:

	==STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR==		==STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR==
	<StructureSection load='2dtr' size='340' side='right' caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dtr' size='340' side='right' caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [http://pdbe.org/2dtr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [http://www.ebi.ac.uk/pdbsum/2dtr 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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [http://pdbe.org/2dtr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [http://www.ebi.ac.uk/pdbsum/2dtr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtr_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtr_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 04:58, 10 February 2016

2016-02-10T04:58:49Z

← Older revision		Revision as of 04:58, 10 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dtr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:36, 11 September 2015

2015-09-11T05:36:39Z

← Older revision		Revision as of 05:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2dtr' size='340' side='right' caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dtr' size='340' side='right' caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Corynebacterium_diphtheriae Corynebacterium~~ diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 ~~Corynebacterium~~ diphtheriae])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [http://www.ebi.ac.uk/pdbsum/2dtr 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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [http://pdbe.org/2dtr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [http://www.ebi.ac.uk/pdbsum/2dtr PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 2dtr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Corynebacterium~~ diphtheriae]]		[[Category: Bacillus diphtheriae kruse in flugge 1886]]
	[[Category: Hol, W G]]		[[Category: Hol, W G]]
	[[Category: Pohl, E]]		[[Category: Pohl, E]]

OCA at 11:56, 25 December 2014

2014-12-25T11:56:27Z

← Older revision		Revision as of 11:56, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTR FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 Corynebacterium diphtheriae])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 Corynebacterium diphtheriae])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [http://www.ebi.ac.uk/pdbsum/2dtr 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=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [http://www.ebi.ac.uk/pdbsum/2dtr PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Corynebacterium diphtheriae]]		[[Category: Corynebacterium diphtheriae]]
	[[Category: Hol, W G.]]		[[Category: Hol, W G]]
	[[Category: Pohl, E.]]		[[Category: Pohl, E]]
	[[Category: Qiu, X.]]		[[Category: Qiu, X]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Repressor]]		[[Category: Repressor]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

OCA at 01:08, 30 September 2014

2014-09-30T01:08:14Z

← Older revision		Revision as of 01:08, 30 September 2014
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	[[Image:~~2dtr~~.~~png~~\|~~left~~\|~~200px~~]]		==STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR==
			<StructureSection load='2dtr' size='340' side='right' caption='[[2dtr]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dtr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTR FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 Corynebacterium diphtheriae])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtr RCSB], [http://www.ebi.ac.uk/pdbsum/2dtr PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtr_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The crystal structure of diphtheria toxin repressor (DtxR) in complex with the corepressor Co2+ has been determined at 2.0 A resolution and in complex with Mn2+ at 2.2 A resolution. The structure of the flexible third domain could be determined at this high resolution. It appears to contain five antiparallel strands exhibiting a fold very similar to the SH3 domain. A superposition of 46 equivalent C alpha atoms of DtxR and alpha-spectrin SH3 resulted in an rms deviation of 3.0 A. The sequence identity is only 7%. This third domain of DtxR appears to have no interactions with the DNA binding domain nor with the metal binding domain of the repressor. Yet, flexibility in the region between the second and the third domain allows in principle significant conformational changes such as might occur upon DNA binding. The two metal binding sites in the second domain have been unraveled in considerable detail. Metal binding site 1 was well occupied in both the cobalt and manganese structures and showed a surprising sulfate ion as ligand. The sulfate was proven beyond doubt by the high peak at its position in a selenate versus sulfate difference Fourier. The presence of the intriguing sulfate ion at such a crucial position near the metal corepressor suggests the possibility that under physiological conditions phosphate may act as a "co-corepressor" for this class of metal-regulated DNA binding proteins in Corynebacteria, Mycobacteria, and related organisms. The second metal binding site is significantly different in these two DtxR structures. In the 2.0 A cobalt structure, the site is not occupied by a metal ion. In the 2.2 A manganese structure the site is well occupied, at approximately the same position as observed previously in cadmium DtxR. The ligands are Glu105, His106, the carbonyl oxygen of Cys102, and a water molecule. The reasons for differential occupancy of this site in different structures are intriguing and require further investigations.

	~~{{STRUCTURE_2dtr\| PDB=2dtr \| SCENE= }}~~		High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor.,Qiu X, Pohl E, Holmes RK, Hol WG Biochemistry. 1996 Sep 24;35(38):12292-302. PMID:8823163<ref>PMID:8823163</ref>

	~~===STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_8823163}}~~		==See Also==
			*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
	==~~About this Structure~~==		== References ==
	[[2dtr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA~~].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:008823163<~~/~~ref><ref group="xtra">PMID:011917145</ref~~><~~ref group="xtra">PMID:015048824</ref><references group="xtra"~~/>
	[[Category: Corynebacterium diphtheriae]]		[[Category: Corynebacterium diphtheriae]]
	[[Category: Hol, W G.]]		[[Category: Hol, W G.]]

OCA: Protected "2dtr" [edit=sysop:move=sysop]

2013-01-06T10:24:28Z

Protected "2dtr" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:24, 6 January 2013
(No difference)

OCA at 10:24, 6 January 2013

2013-01-06T10:24:26Z

← Older revision		Revision as of 10:24, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2dtr.png\|left\|200px]]		[[Image:2dtr.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dtr", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2dtr\| PDB=2dtr \| SCENE= }}		{{STRUCTURE_2dtr\| PDB=2dtr \| SCENE= }}

	===STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR===		===STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_8823163}}, adds the Publication Abstract to the page~~
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	{{ABSTRACT_PUBMED_8823163}}		{{ABSTRACT_PUBMED_8823163}}

	==About this Structure==		==About this Structure==
	~~2DTR~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA].		[[2dtr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~8823163~~</ref><references group="xtra"/>		<ref group="xtra">PMID:008823163</ref><ref group="xtra">PMID:011917145</ref><ref group="xtra">PMID:015048824</ref><references group="xtra"/>
	[[Category: Corynebacterium diphtheriae]]		[[Category: Corynebacterium diphtheriae]]
	[[Category: Hol, W G.]]		[[Category: Hol, W G.]]
Line 32:		Line 20:
	[[Category: Repressor]]		[[Category: Repressor]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:37:10 2009''~~

OCA at 13:37, 17 February 2009

2009-02-17T13:37:11Z

← Older revision		Revision as of 13:37, 17 February 2009
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	==About this Structure==		==About this Structure==
	2DTR is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA].		2DTR is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dtr 1dtr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTR OCA].

	==Reference==		==Reference==
	High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor., Qiu X, Pohl E, Holmes RK, Hol WG, Biochemistry. 1996 Sep 24;35(38):12292-302. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/8823163 8823163]~~		<ref group="xtra">PMID:8823163</ref><references group="xtra"/>
	[[Category: Corynebacterium diphtheriae]]		[[Category: Corynebacterium diphtheriae]]
	~~[[Category: Single protein]]~~
	[[Category: Hol, W G.]]		[[Category: Hol, W G.]]
	[[Category: Pohl, E.]]		[[Category: Pohl, E.]]
Line 34:		Line 33:
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 21~~:20:10 ~~2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:37:10 2009''