1mq7 - Revision history

OCA at 07:47, 14 February 2024

OCA — Wed, 14 Feb 2024 07:47:15 GMT

←Older revision		Revision as of 07:47, 14 February 2024
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	<StructureSection load='1mq7' size='340' side='right'caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1mq7' size='340' side='right'caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE~~-1~~,3-DIOL'>TRS</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]] 1.95Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1773~~ "~~Bacillus tuberculosis~~" ~~(Zopf 1883) Klein 1884])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.6.~~1~~.23~~ 3~~.6.1.23]~~ </~~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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [https://pdbe.org/1mq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [https://www.ebi.ac.uk/pdbsum/1mq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mq7 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [~~http~~://pdbe.org/1mq7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1mq7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1mq7 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DUT_MYCTU DUT_MYCTU]] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.[HAMAP-Rule:MF_00116]	+	[https://www.uniprot.org/uniprot/DUT_MYCTU DUT_MYCTU] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.[HAMAP-Rule:MF_00116]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1mq7 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=1mq7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.
-
-	Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.,Chan S, Segelke B, Lekin T, Krupka H, Cho US, Kim MY, So M, Kim CY, Naranjo CM, Rogers YC, Park MS, Waldo GS, Pashkov I, Cascio D, Perry JL, Sawaya MR J Mol Biol. 2004 Aug 6;341(2):503-17. PMID:15276840<ref>PMID:15276840</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1mq7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[DUTPase 3D structures\|DUTPase 3D structures]]		*[[DUTPase 3D structures\|DUTPase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~DUTP diphosphatase~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Chan, S]]	+	[[Category: Chan S]]
-	[[Category: Cho~~, U S~~]]	+	[[Category: Cho US]]
-	[[Category: Eisenberg, D]]	+	[[Category: Eisenberg D]]
-	[[Category: Heike, K]]	+	[[Category: Heike K]]
-	[[Category: Lekin, T]]	+	[[Category: Lekin T]]
-	[[Category: Naranjo, C]]	+	[[Category: Naranjo C]]
-	[[Category: Perry~~, L J~~]]	+	[[Category: Perry LJ]]
-	[[Category: Sawaya~~, M R~~]]	+	[[Category: Sawaya MR]]
-	[[Category: Segelke~~, B W]]~~	+	[[Category: Segelke BW]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Yeates TO]]
-	[[Category: Yeates~~, T O]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Jelly-roll]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Tbsgc~~]]	+

OCA at 08:40, 2 December 2020

OCA — Wed, 02 Dec 2020 08:40:15 GMT

←Older revision		Revision as of 08:40, 2 December 2020
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	==CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)==		==CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)==
-	<StructureSection load='1mq7' size='340' side='right' caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='1mq7' size='340' side='right'caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://pdbe.org/1mq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mq7 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://pdbe.org/1mq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mq7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1mq7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1mq7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DUTPase 3D structures\|DUTPase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]
	[[Category: Chan, S]]		[[Category: Chan, S]]

OCA at 08:10, 31 January 2018

OCA — Wed, 31 Jan 2018 08:10:31 GMT

←Older revision		Revision as of 08:10, 31 January 2018
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		+
	==CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)==		==CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)==
	<StructureSection load='1mq7' size='340' side='right' caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1mq7' size='340' side='right' caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://pdbe.org/1mq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://pdbe.org/1mq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mq7 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/mq/1mq7_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mq/1mq7_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 1mq7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1mq7" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase\|Deoxyuridine 5'-triphosphate nucleotidohydrolase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:40, 7 February 2016

OCA — Sun, 07 Feb 2016 05:40:08 GMT

←Older revision		Revision as of 05:40, 7 February 2016
Line 18:		Line 18:
	<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=1mq7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:23, 9 September 2015

OCA — Wed, 09 Sep 2015 22:23:20 GMT

←Older revision		Revision as of 22:23, 9 September 2015
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	<StructureSection load='1mq7' size='340' side='right' caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1mq7' size='340' side='right' caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://pdbe.org/1mq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 1mq7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]
	[[Category: Chan, S]]		[[Category: Chan, S]]

OCA at 08:18, 24 December 2014

OCA — Wed, 24 Dec 2014 08:18:00 GMT

←Older revision		Revision as of 08:18, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DUT_MYCTU DUT_MYCTU]] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.[HAMAP-Rule:MF_00116]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]
-	[[Category: Chan, S.]]	+	[[Category: Chan, S]]
-	[[Category: Cho, U S.]]	+	[[Category: Cho, U S]]
-	[[Category: Eisenberg, D.]]	+	[[Category: Eisenberg, D]]
-	[[Category: Heike, K.]]	+	[[Category: Heike, K]]
-	[[Category: Lekin, T.]]	+	[[Category: Lekin, T]]
-	[[Category: Naranjo, C.]]	+	[[Category: Naranjo, C]]
-	[[Category: Perry, L J.]]	+	[[Category: Perry, L J]]
-	[[Category: Sawaya, M R.]]	+	[[Category: Sawaya, M R]]
-	[[Category: Segelke, B W.]]	+	[[Category: Segelke, B W]]
-	[[Category: ~~TBSGC, TB~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Yeates, T O.]]	+	[[Category: Yeates, T O]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Jelly-roll]]		[[Category: Jelly-roll]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Tb structural genomics consortium~~]]	+
	[[Category: Tbsgc]]		[[Category: Tbsgc]]

OCA at 14:05, 28 September 2014

OCA — Sun, 28 Sep 2014 14:05:51 GMT

←Older revision		Revision as of 14:05, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1mq7.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)==
		+	<StructureSection load='1mq7' size='340' side='right' caption='[[1mq7]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MQ7 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2697c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </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=1mq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1mq7 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/mq/1mq7_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 structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.

-	~~{{STRUCTURE_1mq7\| PDB=1mq7 \| SCENE= }}~~	+	Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.,Chan S, Segelke B, Lekin T, Krupka H, Cho US, Kim MY, So M, Kim CY, Naranjo CM, Rogers YC, Park MS, Waldo GS, Pashkov I, Cascio D, Perry JL, Sawaya MR J Mol Biol. 2004 Aug 6;341(2):503-17. PMID:15276840<ref>PMID:15276840</ref>

-	~~===CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15276840}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1mq7]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA].~~	+

	==See Also==		==See Also==
	*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase\|Deoxyuridine 5'-triphosphate nucleotidohydrolase]]		*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase\|Deoxyuridine 5'-triphosphate nucleotidohydrolase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015276840<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]

OCA at 05:44, 20 October 2012

OCA — Sat, 20 Oct 2012 05:44:43 GMT

←Older revision		Revision as of 05:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1mq7]] is a 1 chain structure ~~of [[Deoxyuridine 5'-triphosphate nucleotidohydrolase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA].	+	[[1mq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA].

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

OCA: Protected "1mq7" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 10:59:05 GMT

Protected "1mq7" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:59, 25 July 2012

OCA at 10:59, 25 July 2012

OCA — Wed, 25 Jul 2012 10:59:04 GMT

←Older revision		Revision as of 10:59, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1mq7.png\|left\|200px]]		[[Image:1mq7.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1mq7", 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.
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	{{STRUCTURE_1mq7\| PDB=1mq7 \| SCENE= }}		{{STRUCTURE_1mq7\| PDB=1mq7 \| SCENE= }}

	===CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)===		===CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15276840}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15276840 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15276840}}		{{ABSTRACT_PUBMED_15276840}}

	==About this Structure==		==About this Structure==
-	~~1MQ7~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA].	+	[[1mq7]] is a 1 chain structure of [[Deoxyuridine 5'-triphosphate nucleotidohydrolase]] with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MQ7 OCA].
		+
		+	==See Also==
		+	*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase\|Deoxyuridine 5'-triphosphate nucleotidohydrolase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15276840~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015276840</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: DUTP diphosphatase]]		[[Category: DUTP diphosphatase]]
Line 37:		Line 28:
	[[Category: TBSGC, TB Structural Genomics Consortium.]]		[[Category: TBSGC, TB Structural Genomics Consortium.]]
	[[Category: Yeates, T O.]]		[[Category: Yeates, T O.]]
		+	[[Category: Hydrolase]]
	[[Category: Jelly-roll]]		[[Category: Jelly-roll]]
	[[Category: Protein structure initiative]]		[[Category: Protein structure initiative]]
Line 43:		Line 35:
	[[Category: Tb structural genomics consortium]]		[[Category: Tb structural genomics consortium]]
	[[Category: Tbsgc]]		[[Category: Tbsgc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:41:55 2009''