1k3x - Revision history

OCA at 08:50, 16 August 2023

OCA — Wed, 16 Aug 2023 08:50:43 GMT

←Older revision		Revision as of 08:50, 16 August 2023
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	<StructureSection load='1k3x' size='340' side='right'caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1k3x' size='340' side='right'caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k3x]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1K3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k3x]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K3X FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.25Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [https://pdbe.org/1k3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [https://www.ebi.ac.uk/pdbsum/1k3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3x 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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [~~http~~://pdbe.org/1k3x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1k3x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3x ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/END8_ECOLI END8_ECOLI]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Acts on DNA bubble and 3'-fork structures, suggesting a role in replication-associated DNA repair. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.<ref>PMID:20031487</ref>	+	[https://www.uniprot.org/uniprot/END8_ECOLI END8_ECOLI] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Acts on DNA bubble and 3'-fork structures, suggesting a role in replication-associated DNA repair. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.<ref>PMID:20031487</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]		*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fernandes~~, A S~~]]	+	[[Category: Fernandes AS]]
-	[[Category: Gerchman~~, S E~~]]	+	[[Category: Gerchman SE]]
-	[[Category: Gilboa, R]]	+	[[Category: Gilboa R]]
-	[[Category: Golan, G]]	+	[[Category: Golan G]]
-	[[Category: Grollman~~, A P~~]]	+	[[Category: Grollman AP]]
-	[[Category: Kycia~~, J H~~]]	+	[[Category: Kycia JH]]
-	[[Category: Rieger~~, R A~~]]	+	[[Category: Rieger RA]]
-	[[Category: Shoham, G]]	+	[[Category: Shoham G]]
-	[[Category: Zharkov~~, D O]]~~	+	[[Category: Zharkov DO]]
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Hydrolase/dna~~]]	+

OCA at 07:39, 25 November 2020

OCA — Wed, 25 Nov 2020 07:39:45 GMT

←Older revision		Revision as of 07:39, 25 November 2020
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	==Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA==		==Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA==
-	<StructureSection load='1k3x' size='340' side='right' caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='1k3x' size='340' side='right'caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k3x]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1K3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k3x]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1K3X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://pdbe.org/1k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3x 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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://pdbe.org/1k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1k3x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1k3x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Fernandes, A S]]		[[Category: Fernandes, A S]]
	[[Category: Gerchman, S E]]		[[Category: Gerchman, S E]]

OCA at 21:19, 24 January 2018

OCA — Wed, 24 Jan 2018 21:19:30 GMT

←Older revision		Revision as of 21:19, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA==		==Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA==
	<StructureSection load='1k3x' size='340' side='right' caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1k3x' size='340' side='right' caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://pdbe.org/1k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x 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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://pdbe.org/1k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3x 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/k3/1k3x_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k3/1k3x_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1k3x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1k3x" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]
-	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:44, 10 February 2016

OCA — Wed, 10 Feb 2016 02:44:43 GMT

←Older revision		Revision as of 02:44, 10 February 2016
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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=1k3x ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:35, 11 September 2015

OCA — Fri, 11 Sep 2015 04:35:57 GMT

←Older revision		Revision as of 04:35, 11 September 2015
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	<StructureSection load='1k3x' size='340' side='right' caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1k3x' size='340' side='right' caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k3x]] is a 3 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=1K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k3x]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K3X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nei ([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">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x 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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://pdbe.org/1k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x 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 1k3x" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Fernandes, A S]]		[[Category: Fernandes, A S]]
	[[Category: Gerchman, S E]]		[[Category: Gerchman, S E]]

OCA at 11:14, 25 December 2014

OCA — Thu, 25 Dec 2014 11:14:25 GMT

←Older revision		Revision as of 11:14, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k3x]] is a 3 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=1K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K3X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k3x]] is a 3 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=1K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K3X FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nei ([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">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x 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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/END8_ECOLI END8_ECOLI]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Acts on DNA bubble and 3'-fork structures, suggesting a role in replication-associated DNA repair. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.<ref>PMID:20031487</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Fernandes, A S.]]	+	[[Category: Fernandes, A S]]
-	[[Category: Gerchman, S E.]]	+	[[Category: Gerchman, S E]]
-	[[Category: Gilboa, R.]]	+	[[Category: Gilboa, R]]
-	[[Category: Golan, G.]]	+	[[Category: Golan, G]]
-	[[Category: Grollman, A P.]]	+	[[Category: Grollman, A P]]
-	[[Category: Kycia, J H.]]	+	[[Category: Kycia, J H]]
-	[[Category: Rieger, R A.]]	+	[[Category: Rieger, R A]]
-	[[Category: Shoham, G.]]	+	[[Category: Shoham, G]]
-	[[Category: Zharkov, D O.]]	+	[[Category: Zharkov, D O]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Hydrolase/dna]]		[[Category: Hydrolase/dna]]

OCA at 08:24, 3 October 2014

OCA — Fri, 03 Oct 2014 08:24:24 GMT

←Older revision		Revision as of 08:24, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1k3x.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA==
		+	<StructureSection load='1k3x' size='340' side='right' caption='[[1k3x]], [[Resolution\|resolution]] 1.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1k3x]] is a 3 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=1K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K3X FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k3x RCSB], [http://www.ebi.ac.uk/pdbsum/1k3x 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/k3/1k3x_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 ==
		+	Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. However, Nei differs significantly from Fpg in substrate specificity. We determined the structure of Nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 A resolution. The crosslink is derived from a Schiff base intermediate that precedes beta-elimination and is stabilized by reduction with NaBH(4). Nei consists of two domains connected by a hinge region, creating a DNA binding cleft between domains. DNA in the complex is sharply kinked, the deoxyribitol moiety is bound covalently to Pro1 and everted from the duplex into the active site. Amino acids involved in substrate binding and catalysis are identified. Molecular modeling and analysis of amino acid conservation suggest a site for recognition of the damaged base. Based on structural features of the complex and site-directed mutagenesis studies, we propose a catalytic mechanism for Nei.

-	~~{{STRUCTURE_1k3x\| PDB=1k3x \| SCENE= }}~~	+	Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.,Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G EMBO J. 2002 Feb 15;21(4):789-800. PMID:11847126<ref>PMID:11847126</ref>

-	~~===Crystal structure of~~ a ~~trapped reaction intermediate~~ of the ~~DNA repair enzyme Endonuclease VIII with Brominated-DNA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11847126}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1k3x]] is a 3 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=1K3X OCA].~~	+

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011847126<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Fernandes, A S.]]		[[Category: Fernandes, A S.]]

OCA at 16:03, 20 October 2012

OCA — Sat, 20 Oct 2012 16:03:21 GMT

←Older revision		Revision as of 16:03, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1k3x]] is a 3 chain structure ~~of [[DNA glycosylate]] and [[Endonuclease]]~~ 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=1K3X OCA].	+	[[1k3x]] is a 3 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=1K3X OCA].

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

OCA: Protected "1k3x" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 20:26:59 GMT

Protected "1k3x" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:26, 26 July 2012

OCA at 20:26, 26 July 2012

OCA — Thu, 26 Jul 2012 20:26:58 GMT

←Older revision		Revision as of 20:26, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1k3x.png\|left\|200px]]		[[Image:1k3x.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1k3x", 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_1k3x\| PDB=1k3x \| SCENE= }}		{{STRUCTURE_1k3x\| PDB=1k3x \| SCENE= }}

	===Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA===		===Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11847126}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11847126 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11847126}}		{{ABSTRACT_PUBMED_11847126}}

	==About this Structure==		==About this Structure==
-	~~1K3X~~ is a 3 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3X OCA].	+	[[1k3x]] is a 3 chain structure of [[DNA glycosylate]] and [[Endonuclease]] 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=1K3X OCA].
		+
		+	==See Also==
		+	*[[DNA glycosylate\|DNA glycosylate]]
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11847126~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011847126</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Fernandes, A S.]]		[[Category: Fernandes, A S.]]
Line 34:		Line 26:
	[[Category: Shoham, G.]]		[[Category: Shoham, G.]]
	[[Category: Zharkov, D O.]]		[[Category: Zharkov, D O.]]
		+	[[Category: Hydrolase-dna complex]]
	[[Category: Hydrolase/dna]]		[[Category: Hydrolase/dna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:46:56 2009''