4eug - Revision history

OCA at 15:09, 14 March 2024

2024-03-14T15:09:24Z

← Older revision		Revision as of 15:09, 14 March 2024
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	<StructureSection load='4eug' size='340' side='right'caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4eug' size='340' side='right'caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4eug]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Escherichia_coli_(strain_b)~~ Escherichia coli ~~(strain b)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EUG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4eug]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B Escherichia coli B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EUG FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2eug\|2eug]], [[3eug\|3eug]], [[5eug\|5eug]]</div></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.4Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">UNG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax~~.~~cgi?mode=Info~~&~~srchmode=5&id=37762 Escherichia coli (strain B)])</td></tr>~~
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [https://pdbe.org/4eug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [https://www.ebi.ac.uk/pdbsum/4eug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eug 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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [https://pdbe.org/4eug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [https://www.ebi.ac.uk/pdbsum/4eug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eug ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/UNG_ECOLI UNG_ECOLI]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.[HAMAP-Rule:MF_00148]		[https://www.uniprot.org/uniprot/UNG_ECOLI UNG_ECOLI] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.[HAMAP-Rule:MF_00148]
	== 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=4eug 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=4eug ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The nature of the putative general acid His187 in the reaction catalyzed by Escherichia coli uracil DNA glycosylase (UDG) was investigated using X-ray crystallography and NMR spectroscopy. The crystal structures of H187Q UDG, and its complex with uracil, have been solved at 1.40 and 1.60 A resolution, respectively. The structures are essentially identical to those of the wild-type enzyme, except that the side chain of Gln187 is turned away from the uracil base and cannot interact with uracil O2. This result provides a structural basis for the similar kinetic properties of the H187Q and H187A enzymes. The ionization state of His187 was directly addressed with (1)H-(15)N NMR experiments optimized for histidine ring spin systems, which established that His187 is neutral in the catalytically active state of the enzyme (pK(a) <5.5). These NMR experiments also show that His187 is held in the N(epsilon)()2-H tautomeric form, consistent with the crystallographic observation of a 2.9 A hydrogen bond from the backbone nitrogen of Ser189 to the ring N(delta)()1 of His187. The energetic cost of breaking this hydrogen bond may contribute significantly to the low pK(a) of His187. Thus, the traditional view that a cationic His187 donates a proton to uracil O2 is incorrect. Rather, we propose a concerted mechanism involving general base catalysis by Asp64 and electrophilic stabilization of the developing enolate on uracil O2 by a neutral His187.

	Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187.,Drohat AC, Xiao G, Tordova M, Jagadeesh J, Pankiewicz KW, Watanabe KA, Gilliland GL, Stivers JT Biochemistry. 1999 Sep 14;38(37):11876-86. PMID:10508390<ref>PMID:10508390</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4eug" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Escherichia coli B]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Uridine nucleosidase]]~~		[[Category: Drohat AC]]
	[[Category: Drohat~~, A C~~]]		[[Category: Gilliland GL]]
	[[Category: Gilliland~~, G L~~]]		[[Category: Jagadeesh J]]
	[[Category: Jagadeesh, J]]		[[Category: Stivers JT]]
	[[Category: Stivers~~, J T~~]]		[[Category: Tordova M]]
	[[Category: Tordova, M]]		[[Category: Xiao G]]
	[[Category: Xiao, G]]
	~~[[Category: Glycosylase]]~~
	~~[[Category: Hydrolase~~]]

OCA at 15:49, 3 November 2021

2021-11-03T15:49:15Z

← Older revision		Revision as of 15:49, 3 November 2021
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	==Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex==		==Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex==
	<StructureSection load='4eug' size='340' side='right' caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4eug' size='340' side='right'caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4eug]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli_(strain_b) Escherichia coli (strain b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EUG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4EUG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4eug]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_(strain_b) Escherichia coli (strain b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EUG FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eug\|2eug]], [[3eug\|3eug]], [[5eug\|5eug]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2eug\|2eug]], [[3eug\|3eug]], [[5eug\|5eug]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37762 Escherichia coli (strain B)])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37762 Escherichia coli (strain B)])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [~~http~~://pdbe.org/4eug PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4eug PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4eug 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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [https://pdbe.org/4eug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [https://www.ebi.ac.uk/pdbsum/4eug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eug ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/UNG_ECOLI UNG_ECOLI]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.[HAMAP-Rule:MF_00148]		[[https://www.uniprot.org/uniprot/UNG_ECOLI UNG_ECOLI]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.[HAMAP-Rule:MF_00148]
	== 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: Large Structures]]
	[[Category: Uridine nucleosidase]]		[[Category: Uridine nucleosidase]]
	[[Category: Drohat, A C]]		[[Category: Drohat, A C]]

OCA at 06:46, 14 March 2018

2018-03-14T06:46:30Z

← Older revision		Revision as of 06:46, 14 March 2018
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	==Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex==		==Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex==
	<StructureSection load='4eug' size='340' side='right' caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4eug' size='340' side='right' caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37762 Escherichia coli (strain B)])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37762 Escherichia coli (strain B)])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [http://pdbe.org/4eug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [http://www.ebi.ac.uk/pdbsum/4eug 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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [http://pdbe.org/4eug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [http://www.ebi.ac.uk/pdbsum/4eug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4eug 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/eu/4eug_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/4eug_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 4eug" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4eug" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA glycosylase\|DNA glycosylase]]
	*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:15, 9 February 2016

2016-02-09T02:15:00Z

← Older revision		Revision as of 02:15, 9 February 2016
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	<StructureSection load='4eug' size='340' side='right' caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4eug' size='340' side='right' caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4eug]] is a 1 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=4EUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EUG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4eug]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_(strain_b) Escherichia coli (strain b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EUG FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eug\|2eug]], [[3eug\|3eug]], [[5eug\|5eug]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eug\|2eug]], [[3eug\|3eug]], [[5eug\|5eug]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562~~ Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37762 Escherichia coli (strain B)])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [http://www.ebi.ac.uk/pdbsum/4eug 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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [http://pdbe.org/4eug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [http://www.ebi.ac.uk/pdbsum/4eug PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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=4eug 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 4eug" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Escherichia coli]]~~
	[[Category: Uridine nucleosidase]]		[[Category: Uridine nucleosidase]]
	[[Category: Drohat, A C]]		[[Category: Drohat, A C]]

OCA at 03:43, 25 December 2014

2014-12-25T03:43:00Z

← Older revision		Revision as of 03:43, 25 December 2014
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	[[Image:~~4eug~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex==
			<StructureSection load='4eug' size='340' side='right' caption='[[4eug]], [[Resolution\|resolution]] 1.40Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4eug]] is a 1 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=4EUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EUG FirstGlance]. <br>
			</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2eug\|2eug]], [[3eug\|3eug]], [[5eug\|5eug]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [http://www.ebi.ac.uk/pdbsum/4eug PDBsum]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/UNG_ECOLI UNG_ECOLI]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.[HAMAP-Rule:MF_00148]
			== 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/eu/4eug_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 nature of the putative general acid His187 in the reaction catalyzed by Escherichia coli uracil DNA glycosylase (UDG) was investigated using X-ray crystallography and NMR spectroscopy. The crystal structures of H187Q UDG, and its complex with uracil, have been solved at 1.40 and 1.60 A resolution, respectively. The structures are essentially identical to those of the wild-type enzyme, except that the side chain of Gln187 is turned away from the uracil base and cannot interact with uracil O2. This result provides a structural basis for the similar kinetic properties of the H187Q and H187A enzymes. The ionization state of His187 was directly addressed with (1)H-(15)N NMR experiments optimized for histidine ring spin systems, which established that His187 is neutral in the catalytically active state of the enzyme (pK(a) <5.5). These NMR experiments also show that His187 is held in the N(epsilon)()2-H tautomeric form, consistent with the crystallographic observation of a 2.9 A hydrogen bond from the backbone nitrogen of Ser189 to the ring N(delta)()1 of His187. The energetic cost of breaking this hydrogen bond may contribute significantly to the low pK(a) of His187. Thus, the traditional view that a cationic His187 donates a proton to uracil O2 is incorrect. Rather, we propose a concerted mechanism involving general base catalysis by Asp64 and electrophilic stabilization of the developing enolate on uracil O2 by a neutral His187.

	~~{{STRUCTURE_4eug\| PDB=4eug \| SCENE= }}~~		Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187.,Drohat AC, Xiao G, Tordova M, Jagadeesh J, Pankiewicz KW, Watanabe KA, Gilliland GL, Stivers JT Biochemistry. 1999 Sep 14;38(37):11876-86. PMID:10508390<ref>PMID:10508390</ref>

	~~===Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures~~ of ~~Mutant H187Q and its Uracil Complex===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_10508390}}~~

	~~==About this Structure==~~
	~~[[4eug]] is a 1 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=4EUG OCA].~~

	==See Also==		==See Also==
	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]		*[[DNA glycosylase\|DNA glycosylase]]
			*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]
	==~~Reference~~==		== References ==
	<~~ref group="xtra">PMID:010508390<~~/~~ref~~><~~references group="xtra"~~/>		<references/>
			__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Uridine nucleosidase]]		[[Category: Uridine nucleosidase]]
	[[Category: Drohat, A C.]]		[[Category: Drohat, A C]]
	[[Category: Gilliland, G L.]]		[[Category: Gilliland, G L]]
	[[Category: Jagadeesh, J.]]		[[Category: Jagadeesh, J]]
	[[Category: Stivers, J T.]]		[[Category: Stivers, J T]]
	[[Category: Tordova, M.]]		[[Category: Tordova, M]]
	[[Category: Xiao, G.]]		[[Category: Xiao, G]]
	[[Category: Glycosylase]]		[[Category: Glycosylase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 12:17, 20 October 2012

2012-10-20T12:17:47Z

← Older revision		Revision as of 12:17, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[4eug]] is a 1 chain structure ~~of [[DNA glycosylate]]~~ 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=4EUG OCA].		[[4eug]] is a 1 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=4EUG OCA].

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

OCA: Protected "4eug" [edit=sysop:move=sysop]

2012-07-26T08:16:20Z

Protected "4eug" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:16, 26 July 2012
(No difference)

OCA at 08:16, 26 July 2012

2012-07-26T08:16:18Z

← Older revision		Revision as of 08:16, 26 July 2012
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	~~{{Seed}}~~
	[[Image:4eug.png\|left\|200px]]		[[Image:4eug.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_4eug", 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_4eug\| PDB=4eug \| SCENE= }}		{{STRUCTURE_4eug\| PDB=4eug \| SCENE= }}

	===~~CRYSTALLOGRAPHIC AND ENZYMATIC STUDIES OF AN ACTIVE SITE VARIANT~~ H187Q ~~OF ESCHERICHIA COLI URACIL~~ DNA ~~GLYCOSYLASE~~: ~~CRYSTAL STRUCTURES OF MUTANT~~ H187Q ~~AND ITS URACIL COMPLEX~~===		===Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex===

			{{ABSTRACT_PUBMED_10508390}}

	~~<!--~~		==About this Structure==
	~~The line below~~ this ~~paragraph, {{ABSTRACT_PUBMED_10090282}}, adds the Publication Abstract to the page~~		[[4eug]] is a 1 chain structure of [[DNA glycosylate]] 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=4EUG OCA].
	~~(as it appears on PubMed at~~ http://~~www~~.~~pubmed~~.~~gov), where 10090282~~ is ~~the PubMed ID number~~.
	-->
	~~{{ABSTRACT_PUBMED_10090282}}~~

	==~~About this Structure~~==		==See Also==
	~~4EUG is a 1 chain 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=4EUG OCA~~].		*[[DNA glycosylate\|DNA glycosylate]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~10090282~~</ref><references group="xtra"/>		<ref group="xtra">PMID:010508390</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Uridine nucleosidase]]		[[Category: Uridine nucleosidase]]
Line 33:		Line 24:
	[[Category: Xiao, G.]]		[[Category: Xiao, G.]]
	[[Category: Glycosylase]]		[[Category: Glycosylase]]
			[[Category: Hydrolase]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 05:38:57 2009''~~

OCA at 03:38, 17 February 2009

2009-02-17T03:38:59Z

← Older revision		Revision as of 03:38, 17 February 2009
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	==About this Structure==		==About this Structure==
	4EUG 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=4EUG OCA].		4EUG is a 1 chain 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=4EUG OCA].

	==Reference==		==Reference==
	Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited., Xiao G, Tordova M, Jagadeesh J, Drohat AC, Stivers JT, Gilliland GL, Proteins. 1999 Apr 1;35(1):13-24. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~10090282 10090282]~~		<ref group="xtra">PMID:10090282</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	~~[[Category: Single protein]]~~
	[[Category: Uridine nucleosidase]]		[[Category: Uridine nucleosidase]]
	[[Category: Drohat, A C.]]		[[Category: Drohat, A C.]]
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	[[Category: Glycosylase]]		[[Category: Glycosylase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 13~~:36:~~20 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:38:57 2009''

OCA at 10:36, 3 July 2008

2008-07-03T10:36:21Z

← Older revision		Revision as of 10:36, 3 July 2008
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	[[Image:4eug.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:4eug.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_4eug\| PDB=4eug \| SCENE= }}		{{STRUCTURE_4eug\| PDB=4eug \| SCENE= }}

	~~'''~~CRYSTALLOGRAPHIC AND ENZYMATIC STUDIES OF AN ACTIVE SITE VARIANT H187Q OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE: CRYSTAL STRUCTURES OF MUTANT H187Q AND ITS URACIL COMPLEX~~'''~~		===CRYSTALLOGRAPHIC AND ENZYMATIC STUDIES OF AN ACTIVE SITE VARIANT H187Q OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE: CRYSTAL STRUCTURES OF MUTANT H187Q AND ITS URACIL COMPLEX===


	~~==Overview==~~		<!--
	The DNA repair enzyme uracil DNA glycosylase (UDG) catalyzes the hydrolysis of premutagenic uracil residues from single-stranded or duplex DNA, producing free uracil and abasic DNA. Here we report the high-resolution crystal structures of free UDG from Escherichia coli strain B (1.60 A), ~~its complex with uracil (1.50 A)~~, ~~and a second active-site complex with glycerol (1.43 A). These represent~~ the ~~first high-resolution structures of a prokaryotic UDG~~ to ~~be reported. The overall structure of~~ the E. ~~coli enzyme is more similar to the human UDG than the herpes virus enzyme~~. ~~Significant differences between the bacterial and viral structures are seen in the side-chain positions of the putative general-acid (His187) and base (Asp64~~), ~~similar to differences previously observed between~~ the ~~viral and human enzymes~~. ~~In general, the active-site loop that contains His187 appears preorganized in comparison with the viral and human enzymes, requiring smaller substrate~~-~~induced conformational changes to bring active~~-site groups into catalytic position. These structural differences may be related to the large differences in the mechanism of uracil recognition used by the E. coli and viral enzymes. The pH dependence of k(cat) for wild-type UDG and the D64N and H187Q mutant enzymes is consistent with general-base catalysis by Asp64, but provides no evidence for a general-acid catalyst. The catalytic mechanism of UDG is critically discussed with respect to these results.		The line below this paragraph, {{ABSTRACT_PUBMED_10090282}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 10090282 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_10090282}}

	==About this Structure==		==About this Structure==
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	[[Category: Xiao, G.]]		[[Category: Xiao, G.]]
	[[Category: Glycosylase]]		[[Category: Glycosylase]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:23:46 2008''
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