1q39 - Revision history

OCA at 09:56, 16 August 2023

OCA — Wed, 16 Aug 2023 09:56:11 GMT

←Older revision		Revision as of 09:56, 16 August 2023
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	<StructureSection load='1q39' size='340' side='right'caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1q39' size='340' side='right'caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q39]] is a 1 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q39]] is a 1 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1q3b\|1q3b]], [[1q3c\|1q3c]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [https://pdbe.org/1q39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [https://www.ebi.ac.uk/pdbsum/1q39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q39 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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [~~http~~://pdbe.org/1q39 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q39 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q39 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: Feinberg, H]]	+	[[Category: Feinberg H]]
-	[[Category: Fernandes~~, A S~~]]	+	[[Category: Fernandes AS]]
-	[[Category: Golan, G]]	+	[[Category: Golan G]]
-	[[Category: Grollman~~, A P~~]]	+	[[Category: Grollman AP]]
-	[[Category: Kycia~~, J H~~]]	+	[[Category: Kycia JH]]
-	[[Category: Shoham, G]]	+	[[Category: Shoham G]]
-	[[Category: Zaika~~, E I~~]]	+	[[Category: Zaika EI]]
-	[[Category: Zharkov~~, D O]]~~	+	[[Category: Zharkov DO]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:42, 9 December 2020

OCA — Wed, 09 Dec 2020 07:42:20 GMT

←Older revision		Revision as of 07:42, 9 December 2020
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	==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.==		==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.==
-	<StructureSection load='1q39' size='340' side='right' caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1q39' size='340' side='right'caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q39]] is a 1 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q39]] is a 1 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q3b\|1q3b]], [[1q3c\|1q3c]]</div></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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://pdbe.org/1q39 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q39 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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://pdbe.org/1q39 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q39 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1q39" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1q39" 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/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Feinberg, H]]		[[Category: Feinberg, H]]
	[[Category: Fernandes, A S]]		[[Category: Fernandes, A S]]

OCA at 08:05, 24 February 2018

OCA — Sat, 24 Feb 2018 08:05:46 GMT

←Older revision		Revision as of 08:05, 24 February 2018
Line 1:		Line 1:
		+
	==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.==		==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.==
	<StructureSection load='1q39' size='340' side='right' caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1q39' size='340' side='right' caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://pdbe.org/1q39 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://pdbe.org/1q39 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q39 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/q3/1q39_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/1q39_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 1q39" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1q39" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]
-	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:53, 8 February 2016

OCA — Mon, 08 Feb 2016 05:53:52 GMT

←Older revision		Revision as of 05:53, 8 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=1q39 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:32, 10 September 2015

OCA — Thu, 10 Sep 2015 08:32:57 GMT

←Older revision		Revision as of 08:32, 10 September 2015
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	<StructureSection load='1q39' size='340' side='right' caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1q39' size='340' side='right' caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q39]] 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q39]] is a 1 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://pdbe.org/1q39 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 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 1q39" 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: Feinberg, H]]		[[Category: Feinberg, H]]
	[[Category: Fernandes, A S]]		[[Category: Fernandes, A S]]

OCA at 21:07, 24 December 2014

OCA — Wed, 24 Dec 2014 21:07:09 GMT

←Older revision		Revision as of 21:07, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q39]] 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q39]] 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 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: Feinberg, H.]]	+	[[Category: Feinberg, H]]
-	[[Category: Fernandes, A S.]]	+	[[Category: Fernandes, A S]]
-	[[Category: Golan, G.]]	+	[[Category: Golan, G]]
-	[[Category: Grollman, A P.]]	+	[[Category: Grollman, A P]]
-	[[Category: Kycia, J H.]]	+	[[Category: Kycia, J H]]
-	[[Category: Shoham, G.]]	+	[[Category: Shoham, G]]
-	[[Category: Zaika, E I.]]	+	[[Category: Zaika, E I]]
-	[[Category: Zharkov, D O.]]	+	[[Category: Zharkov, D O]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 11:10, 3 October 2014

OCA — Fri, 03 Oct 2014 11:10:29 GMT

←Older revision		Revision as of 11:10, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1q39.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.==
		+	<StructureSection load='1q39' size='340' side='right' caption='[[1q39]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1q39]] 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=1Q39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q39 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q3b\|1q3b]], [[1q3c\|1q3c]]</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=1q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q39 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q39 RCSB], [http://www.ebi.ac.uk/pdbsum/1q39 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/q3/1q39_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 ==
		+	Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei-DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 A resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 A) and Nei-R252A (2.05 A). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a approximately 50 degrees rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme.

-	~~{{STRUCTURE_1q39\| PDB=1q39 \| SCENE= }}~~	+	Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.,Golan G, Zharkov DO, Feinberg H, Fernandes AS, Zaika EI, Kycia JH, Grollman AP, Shoham G Nucleic Acids Res. 2005 Sep 6;33(15):5006-16. Print 2005. PMID:16145054<ref>PMID:16145054</ref>

-	~~===Crystal structure~~ of the ~~DNA repair enzyme endonuclease-VIII (Nei) from E~~. ~~coli: The WT enzyme at 2~~.~~8 resolution~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16145054}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1q39]] 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=1Q39 OCA].~~	+

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016145054<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Feinberg, H.]]		[[Category: Feinberg, H.]]

OCA at 09:08, 20 October 2012

OCA — Sat, 20 Oct 2012 09:08:41 GMT

←Older revision		Revision as of 09:08, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1q39]] is a 1 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=1Q39 OCA].	+	[[1q39]] 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=1Q39 OCA].

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

OCA: Protected "1q39" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 21:53:21 GMT

Protected "1q39" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:53, 25 July 2012

OCA at 21:53, 25 July 2012

OCA — Wed, 25 Jul 2012 21:53:19 GMT

←Older revision		Revision as of 21:53, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1q39.png\|left\|200px]]		[[Image:1q39.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1q39", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_1q39\| PDB=1q39 \| SCENE= }}		{{STRUCTURE_1q39\| PDB=1q39 \| SCENE= }}

	===Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.===		===Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16145054}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16145054 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16145054}}		{{ABSTRACT_PUBMED_16145054}}

	==About this Structure==		==About this Structure==
-	~~1Q39~~ 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=1Q39 OCA].	+	[[1q39]] is a 1 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=1Q39 OCA].
		+
		+	==See Also==
		+	*[[DNA glycosylate\|DNA glycosylate]]
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16145054~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016145054</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Feinberg, H.]]		[[Category: Feinberg, H.]]
Line 34:		Line 26:
	[[Category: Zharkov, D O.]]		[[Category: Zharkov, D O.]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:35:08 2009''