5edd - Revision history

OCA at 06:22, 5 July 2023

2023-07-05T06:22:03Z

←Older revision		Revision as of 06:22, 5 July 2023
Line 3:		Line 3:
	<StructureSection load='5edd' size='340' side='right'caption='[[5edd]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='5edd' size='340' side='right'caption='[[5edd]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5edd]] 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=5EDD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EDD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5edd]] 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=5EDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EDD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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]] 1.97Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gcy\|4gcy]], [[3loj\|3loj]], [[3h6d\|3h6d]], [[3hza\|3hza]], [[3i93\|3i93]], [[2py4\|2py4]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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">dut, MRA_2725 ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5edd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edd OCA], [https://pdbe.org/5edd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5edd RCSB], [https://www.ebi.ac.uk/pdbsum/5edd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5edd ProSAT]</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~~://proteopedia.org/fgij/fg.htm?mol=5edd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edd OCA], [~~http~~://pdbe.org/5edd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5edd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5edd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5edd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~DUT_MYCTA DUT_MYCTA]~~] 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.	+	[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~DUTP diphosphatase~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Harmat, V]]	+	[[Category: Harmat V]]
-	[[Category: Leveles, I]]	+	[[Category: Leveles I]]
-	[[Category: Lopata, A]]	+	[[Category: Lopata A]]
-	[[Category: Nagy~~, G N~~]]	+	[[Category: Nagy GN]]
-	[[Category: Toth, J]]	+	[[Category: Toth J]]
-	[[Category: Vertessy~~, G B]]~~	+	[[Category: Vertessy GB]]
-	~~[[Category: Enzyme-ligand complex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Jelly-roll~~]]	+

OCA at 06:54, 22 April 2020

2020-04-22T06:54:21Z

←Older revision		Revision as of 06:54, 22 April 2020
Line 1:		Line 1:

	==Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant==		==Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant==
-	<StructureSection load='5edd' size='340' side='right' caption='[[5edd]], [[Resolution\|resolution]] 1.97Å' scene=''>	+	<StructureSection load='5edd' size='340' side='right'caption='[[5edd]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5edd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EDD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EDD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5edd]] 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=5EDD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EDD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gcy\|4gcy]], [[3loj\|3loj]], [[3h6d\|3h6d]], [[3hza\|3hza]], [[3i93\|3i93]], [[2py4\|2py4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gcy\|4gcy]], [[3loj\|3loj]], [[3h6d\|3h6d]], [[3hza\|3hza]], [[3i93\|3i93]], [[2py4\|2py4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dut, MRA_2725 ([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=5edd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edd OCA], [http://pdbe.org/5edd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edd RCSB], [http://www.ebi.ac.uk/pdbsum/5edd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5edd 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=5edd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edd OCA], [http://pdbe.org/5edd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edd RCSB], [http://www.ebi.ac.uk/pdbsum/5edd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5edd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5edd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5edd" 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: Harmat, V]]		[[Category: Harmat, V]]

OCA at 18:20, 2 November 2016

2016-11-02T18:20:44Z

←Older revision		Revision as of 18:20, 2 November 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5edd is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant==
		+	<StructureSection load='5edd' size='340' side='right' caption='[[5edd]], [[Resolution\|resolution]] 1.97Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5edd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EDD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gcy\|4gcy]], [[3loj\|3loj]], [[3h6d\|3h6d]], [[3hza\|3hza]], [[3i93\|3i93]], [[2py4\|2py4]]</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=5edd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edd OCA], [http://pdbe.org/5edd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edd RCSB], [http://www.ebi.ac.uk/pdbsum/5edd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5edd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DUT_MYCTA DUT_MYCTA]] 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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the gamma-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all the above properties, all essential arginine fingers are used to catalyze the cleavage of the gamma-phosphate. Here, we identify and unveil the role of a conserved arginine residue in trimeric dUTPases that meets all the criteria established for arginine fingers. We found that the conserved arginine adjacent to the P-loop-like motif enables structural organization of the active site for efficient catalysis via its direct nucleotide coordination, while its direct electrostatic role in transition state stabilization is secondary. An exhaustive structure-based comparison of analogous, conserved arginines from nucleotide hydrolases and transferases revealed a consensus amino acid location and orientation for contacting the gamma-phosphate of the substrate nucleotide. Despite the structurally equivalent position, functional differences between arginine fingers of dUTPases and NTPases are explained based on the unique chemistry performed by the pyrophosphatase dUTPases.

-	~~Authors~~: ~~Nagy, G.N~~., ~~Leveles~~, I., Lopata, A., ~~Harmat~~, V., Toth, J., Vertessy, G.B.	+	Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases.,Nagy GN, Suardiaz R, Lopata A, Ozohanics O, Vekey K, Brooks BR, Leveles I, Toth J, Vertessy BG, Rosta E J Am Chem Soc. 2016 Oct 14. PMID:27740761<ref>PMID:27740761</ref>

-	~~Description: Crystal structure of Mycobacterium tuberculosis dUTPase R140K~~, ~~H145W mutant~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Toth, J~~]]	+	<div class="pdbe-citations 5edd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DUTP diphosphatase]]
	[[Category: Harmat, V]]		[[Category: Harmat, V]]
	[[Category: Leveles, I]]		[[Category: Leveles, I]]
	[[Category: Lopata, A]]		[[Category: Lopata, A]]
-	[[Category: Nagy, G.N]]	+	[[Category: Nagy, G N]]
-	[[Category: Vertessy, G.B]]	+	[[Category: Toth, J]]
		+	[[Category: Vertessy, G B]]
		+	[[Category: Enzyme-ligand complex]]
		+	[[Category: Hydrolase]]
		+	[[Category: Jelly-roll]]

OCA: Protected "5edd" [edit=sysop:move=sysop]

2015-12-01T02:40:55Z

Protected "5edd" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:40, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5edd is ON HOLD until Paper Publication Authors: Nagy, G.N., Leveles, I., Lopata, A., Harmat, V., Toth, J., Vertessy, G.B. Description: Crystal str...

2015-12-01T02:40:53Z

New page: '''Unreleased structure''' The entry 5edd is ON HOLD until Paper Publication Authors: Nagy, G.N., Leveles, I., Lopata, A., Harmat, V., Toth, J., Vertessy, G.B. Description: Crystal str...

New page

'''Unreleased structure'''

The entry 5edd is ON HOLD until Paper Publication

Authors: Nagy, G.N., Leveles, I., Lopata, A., Harmat, V., Toth, J., Vertessy, G.B.

Description: Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant
[[Category: Unreleased Structures]]
[[Category: Toth, J]]
[[Category: Harmat, V]]
[[Category: Leveles, I]]
[[Category: Lopata, A]]
[[Category: Nagy, G.N]]
[[Category: Vertessy, G.B]]