2v9x - Revision history

OCA at 15:11, 13 December 2023

OCA — Wed, 13 Dec 2023 15:11:28 GMT

←Older revision		Revision as of 15:11, 13 December 2023
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	<StructureSection load='2v9x' size='340' side='right'caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2v9x' size='340' side='right'caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v9x]] is a 12 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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v9x]] is a 12 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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V9X FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DUT:DEOXYURIDINE~~-~~5-TRIPHOSPHATE'>DUT</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13]~~ </~~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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [https://pdbe.org/2v9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [https://www.ebi.ac.uk/pdbsum/2v9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v9x 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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [https://pdbe.org/2v9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [https://www.ebi.ac.uk/pdbsum/2v9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v9x ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DCD_ECOLI DCD_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: DCTP deaminase]]~~	+	[[Category: Johansson E]]
-	[[Category: Johansson, E]]	+	[[Category: Larsen S]]
-	[[Category: Larsen, S]]	+	[[Category: Thymark M]]
-	[[Category: Thymark, M]]	+	[[Category: Willemoes M]]
-	[[Category: Willemoes, M]]	+
-	~~[[Category: Dctp deaminase]]~~	+
-	~~[[Category: Dutpase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nucleotide metabolism~~]]	+

OCA at 20:58, 20 October 2021

OCA — Wed, 20 Oct 2021 20:58:56 GMT

←Older revision		Revision as of 20:58, 20 October 2021
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	<StructureSection load='2v9x' size='340' side='right'caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2v9x' size='340' side='right'caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [~~http~~://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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2V9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v9x]] is a 12 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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V9X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [~~http~~://pdbe.org/2v9x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2v9x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2v9x 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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [https://pdbe.org/2v9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [https://www.ebi.ac.uk/pdbsum/2v9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v9x ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 14:19, 18 December 2019

OCA — Wed, 18 Dec 2019 14:19:44 GMT

←Older revision		Revision as of 14:19, 18 December 2019
Line 1:		Line 1:

	==E138D variant of Escherichia coli dCTP deaminase in complex with dUTP==		==E138D variant of Escherichia coli dCTP deaminase in complex with dUTP==
-	<StructureSection load='2v9x' size='340' side='right' caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2v9x' size='340' side='right'caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [http://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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V9X FirstGlance]. <br>		<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [http://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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V9X FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 2v9x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2v9x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: DCTP deaminase]]		[[Category: DCTP deaminase]]
	[[Category: Johansson, E]]		[[Category: Johansson, E]]

OCA at 07:27, 17 January 2018

OCA — Wed, 17 Jan 2018 07:27:01 GMT

←Older revision		Revision as of 07:27, 17 January 2018
Line 1:		Line 1:
-	==E138D ~~VARIANT OF ESCHERICHIA COLI DCTP DEAMINASE IN COMPLEX WITH DUTP~~==	+
		+	==E138D variant of Escherichia coli dCTP deaminase in complex with dUTP==
	<StructureSection load='2v9x' size='340' side='right' caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2v9x' size='340' side='right' caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [http://pdbe.org/2v9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [http://www.ebi.ac.uk/pdbsum/2v9x 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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [http://pdbe.org/2v9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [http://www.ebi.ac.uk/pdbsum/2v9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v9x ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/v9/2v9x_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/2v9x_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>
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	</div>		</div>
	<div class="pdbe-citations 2v9x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2v9x" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Deaminase\|Deaminase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:27, 7 February 2016

OCA — Sun, 07 Feb 2016 03:27:48 GMT

←Older revision		Revision as of 03:27, 7 February 2016
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	<StructureSection load='2v9x' size='340' side='right' caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2v9x' size='340' side='right' caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [http://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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V9X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [http://www.ebi.ac.uk/pdbsum/2v9x 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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [http://pdbe.org/2v9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [http://www.ebi.ac.uk/pdbsum/2v9x PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=2v9x ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2v9x" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: DCTP deaminase]]		[[Category: DCTP deaminase]]
	[[Category: Johansson, E]]		[[Category: Johansson, E]]

OCA at 14:17, 19 January 2015

OCA — Mon, 19 Jan 2015 14:17:52 GMT

←Older revision		Revision as of 14:17, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V9X FirstGlance]. <br>		<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V9X FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </span></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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [http://www.ebi.ac.uk/pdbsum/2v9x 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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [http://www.ebi.ac.uk/pdbsum/2v9x PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: DCTP deaminase]]		[[Category: DCTP deaminase]]
-	[[Category: Johansson, E.]]	+	[[Category: Johansson, E]]
-	[[Category: Larsen, S.]]	+	[[Category: Larsen, S]]
-	[[Category: Thymark, M.]]	+	[[Category: Thymark, M]]
-	[[Category: Willemoes, M.]]	+	[[Category: Willemoes, M]]
	[[Category: Dctp deaminase]]		[[Category: Dctp deaminase]]
	[[Category: Dutpase]]		[[Category: Dutpase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nucleotide metabolism]]		[[Category: Nucleotide metabolism]]

OCA at 01:40, 1 October 2014

OCA — Wed, 01 Oct 2014 01:40:10 GMT

←Older revision		Revision as of 01:40, 1 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2v9x.~~png~~\|~~left~~\|200px]]	+	==E138D VARIANT OF ESCHERICHIA COLI DCTP DEAMINASE IN COMPLEX WITH DUTP==
		+	<StructureSection load='2v9x' size='340' side='right' caption='[[2v9x]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2v9x]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V9X FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xs1\|1xs1]], [[1xs4\|1xs4]], [[1xs6\|1xs6]], [[2j4h\|2j4h]], [[2j4q\|2j4q]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] </span></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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [http://www.ebi.ac.uk/pdbsum/2v9x 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/v9/2v9x_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 ==
		+	In Escherichia coli and Salmonella typhimurium about 80% of the dUMP used for dTMP synthesis is derived from deamination of dCTP. The dCTP deaminase produces dUTP that subsequently is hydrolyzed by dUTPase to dUMP and diphosphate. The dCTP deaminase is regulated by dTTP that inhibits the enzyme by binding to the active site and induces an inactive conformation of the trimeric enzyme. We have analyzed the role of residues previously suggested to play a role in catalysis. The mutant enzymes R115Q, S111C, S111T and E138D were all purified and analyzed for activity. Only S111T and E138D displayed detectable activity with a 30- and 140-fold reduction in k(cat), respectively. Furthermore, S111T and E138D both showed altered dTTP inhibition compared to wild-type enzyme. S111T was almost insensitive to the presence of dTTP. With the E138D enzyme the dTTP dependent increase in cooperativity of dCTP saturation was absent, although the dTTP inhibition itself was still cooperative. Modeling of the active site of the S111T enzyme indicated that this enzyme is restricted in forming the inactive dTTP binding conformer due to steric hindrance by the additional methyl group in threonine. The crystal structure of E138D in complex with dUTP showed a hydrogen bonding network in the active site similar to wild-type enzyme. However, changes in the hydrogen bond lengths between the carboxylate and a catalytic water molecule as well as a slightly different orientation of the pyrimidine ring of the bound nucleotide may provide an explanation for the reduced activity.

-	~~{{STRUCTURE_2v9x\| PDB=2v9x \| SCENE= }}~~	+	Mutational analysis of the nucleotide binding site of Escherichia coli dCTP deaminase.,Thymark M, Johansson E, Larsen S, Willemoes M Arch Biochem Biophys. 2008 Feb 1;470(1):20-6. Epub 2007 Oct 30. PMID:17996716<ref>PMID:17996716</ref>

-	~~===E138D VARIANT OF ESCHERICHIA COLI DCTP DEAMINASE IN COMPLEX WITH DUTP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_17996716}}~~	+	==See Also==
-		+	*[[Deaminase\|Deaminase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2v9x~~]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:017996716<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: DCTP deaminase]]		[[Category: DCTP deaminase]]

OCA: Protected "2v9x" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 18:20:05 GMT

Protected "2v9x" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:20, 7 January 2013

OCA at 18:20, 7 January 2013

OCA — Mon, 07 Jan 2013 18:20:03 GMT

←Older revision		Revision as of 18:20, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2v9x.png\|left\|200px]]		[[Image:2v9x.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2v9x", 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_2v9x\| PDB=2v9x \| SCENE= }}		{{STRUCTURE_2v9x\| PDB=2v9x \| SCENE= }}

	===E138D VARIANT OF ESCHERICHIA COLI DCTP DEAMINASE IN COMPLEX WITH DUTP===		===E138D VARIANT OF ESCHERICHIA COLI DCTP DEAMINASE IN COMPLEX WITH DUTP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17996716}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17996716 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17996716}}		{{ABSTRACT_PUBMED_17996716}}

	==About this Structure==		==About this Structure==
-	~~2V9X~~ is a 12 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA].	+	[[2v9x]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17996716~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017996716</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: DCTP deaminase]]		[[Category: DCTP deaminase]]
Line 34:		Line 22:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nucleotide metabolism]]		[[Category: Nucleotide metabolism]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:47:39 2009''

OCA at 08:47, 16 February 2009

OCA — Mon, 16 Feb 2009 08:47:40 GMT

←Older revision		Revision as of 08:47, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2V9X is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA].	+	2V9X is a 12 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X OCA].

	==Reference==		==Reference==
-	~~Mutational analysis of the nucleotide binding site of Escherichia coli dCTP deaminase., Thymark M, Johansson E, Larsen S, Willemoes M, Arch Biochem Biophys. 2008 Feb 1;470(1):20-6. Epub 2007 Oct 30.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17996716 17996716]~~	+	<ref group="xtra">PMID:17996716</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: DCTP deaminase]]		[[Category: DCTP deaminase]]
	[[Category: Johansson, E.]]		[[Category: Johansson, E.]]
Line 36:		Line 35:
	[[Category: Nucleotide metabolism]]		[[Category: Nucleotide metabolism]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 12~~:57:~~45 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:47:39 2009''