1ui1 - Revision history

OCA at 23:54, 27 December 2023

2023-12-27T23:54:03Z

←Older revision		Revision as of 23:54, 27 December 2023
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	<StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]<~~/~~b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[1ui0\|1ui0]]~~</~~div~~>~~</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [https://pdbe.org/1ui1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [https://pdbe.org/1ui1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/UDGA_THET8 UDGA_THET8] Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair as well as from single-stranded DNA (PubMed:12000829, PubMed:14556741). Specifically recognizes uracil that is flipped out from double-stranded DNA (PubMed:14556741).<ref>PMID:12000829</ref> <ref>PMID:14556741</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hoseki, J]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Inoue, Y]]	+	[[Category: Hoseki J]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Inoue Y]]
-	[[Category: Masui, R]]	+	[[Category: Kuramitsu S]]
-	[[Category: Okamoto, A]]	+	[[Category: Masui R]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Okamoto A]]
-	[[Category: Shibata, T]]	+	[[Category: Shibata T]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Base excision repair]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Iron/sulfer cluster]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Thermophile]]~~	+
-	~~[[Category: Uracil-dna glycosylase~~]]	+

OCA at 15:12, 2 June 2021

2021-06-02T15:12:08Z

←Older revision		Revision as of 15:12, 2 June 2021
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	<StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ui0\|1ui0]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [~~http~~://pdbe.org/1ui1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [https://pdbe.org/1ui1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 15:45, 28 August 2019

2019-08-28T15:45:31Z

←Older revision		Revision as of 15:45, 28 August 2019
Line 1:		Line 1:

	==Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8==		==Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8==
-	<StructureSection load='1ui1' size='340' side='right' caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Hoseki, J]]		[[Category: Hoseki, J]]
	[[Category: Inoue, Y]]		[[Category: Inoue, Y]]

OCA at 10:03, 30 January 2019

2019-01-30T10:03:57Z

←Older revision		Revision as of 10:03, 30 January 2019
Line 1:		Line 1:
		+
	==Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8==		==Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8==
	<StructureSection load='1ui1' size='340' side='right' caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1ui1' size='340' side='right' caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [http://pdbe.org/1ui1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [http://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [http://pdbe.org/1ui1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [http://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ui/1ui1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ui/1ui1_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>
Line 31:		Line 32:
	==See Also==		==See Also==
	*[[DNA glycosylase\|DNA glycosylase]]		*[[DNA glycosylase\|DNA glycosylase]]
-	*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:53, 9 February 2016

2016-02-09T18:53:31Z

←Older revision		Revision as of 18:53, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ui1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:05, 11 September 2015

2015-09-11T01:05:57Z

←Older revision		Revision as of 01:05, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ui1' size='340' side='right' caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1ui1' size='340' side='right' caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 ~~Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [http://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [http://pdbe.org/1ui1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [http://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1ui1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Hoseki, J]]		[[Category: Hoseki, J]]
	[[Category: Inoue, Y]]		[[Category: Inoue, Y]]

OCA at 13:40, 6 January 2015

2015-01-06T13:40:50Z

←Older revision		Revision as of 13:40, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [http://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [http://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Hoseki, J.]]	+	[[Category: Hoseki, J]]
-	[[Category: Inoue, Y.]]	+	[[Category: Inoue, Y]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Masui, R.]]	+	[[Category: Masui, R]]
-	[[Category: Okamoto, A.]]	+	[[Category: Okamoto, A]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Shibata, T.]]	+	[[Category: Shibata, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Base excision repair]]		[[Category: Base excision repair]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Iron/sulfer cluster]]		[[Category: Iron/sulfer cluster]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Thermophile]]		[[Category: Thermophile]]
	[[Category: Uracil-dna glycosylase]]		[[Category: Uracil-dna glycosylase]]

OCA at 09:56, 3 October 2014

2014-10-03T09:56:11Z

←Older revision		Revision as of 09:56, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1ui1.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8==
		+	<StructureSection load='1ui1' size='340' side='right' caption='[[1ui1]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UI1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ui0\|1ui0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tthudg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [http://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</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/ui/1ui1_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 ==
		+	Uracil-DNA glycosylase (UDG; EC 3.2.2.-) removes uracil from DNA to initiate DNA base excision repair. Since hydrolytic deamination of cytosine to uracil is one of the most frequent DNA-damaging events in all cells, UDG is an essential enzyme for maintaining the integrity of genomic information. For the first time, we report the crystal structure of a family 4 UDG from Thermus thermophilus HB8 (TthUDG) complexed with uracil, solved at 1.5 angstroms resolution. As opposed to UDG enzymes in its other families, TthUDG possesses a [4Fe-4S] cluster. This iron-sulfur cluster, which is distant from the active site, interacts with loop structures and has been suggested to be unessential to the activity but necessary for stabilizing the loop structures. In addition to the iron-sulfur cluster, salt-bridges and ion pairs on the molecular surface and the presence of proline on loops and turns is thought to contribute to the enzyme's thermostability. Despite very low levels of sequence identity with Escherichia coli and human UDGs (family 1) and E.coli G:T/U mismatch-specific DNA glycosylase (MUG) (family 2), the topology and order of secondary structures of TthUDG are similar to those of these distant relatives. Furthermore, the coordinates of the core structure formed by beta-strands are almost the same. Positive charge is distributed over the active-site groove, where TthUDG would bind DNA strands, as do UDG enzymes in other families. TthUDG recognizes uracil specifically in the same manner as does human UDG (family 1), rather than guanine in the complementary strand DNA, as does E.coli MUG (family 2). These results suggest that the mechanism by which family 4 UDGs remove uracils from DNA is similar to that of family 1 enzymes.

-	~~{{STRUCTURE_1ui1\| PDB=1ui1 \| SCENE= }}~~	+	Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8.,Hoseki J, Okamoto A, Masui R, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S J Mol Biol. 2003 Oct 24;333(3):515-26. PMID:14556741<ref>PMID:14556741</ref>

-	~~===Crystal Structure Of Uracil-DNA Glycosylase~~ From ~~Thermus Thermophilus HB8===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14556741}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ui1]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 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:014556741<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Hoseki, J.]]		[[Category: Hoseki, J.]]

OCA at 14:48, 20 October 2012

2012-10-20T14:48:37Z

←Older revision		Revision as of 14:48, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ui1]] is a 1 chain structure ~~of [[DNA glycosylate]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA].	+	[[1ui1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UI1 OCA].

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

OCA: Protected "1ui1" [edit=sysop:move=sysop]

2012-07-26T16:19:48Z

Protected "1ui1" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:19, 26 July 2012