2f5n - Revision history

OCA at 07:43, 23 August 2023

2023-08-23T07:43:28Z

←Older revision		Revision as of 07:43, 23 August 2023
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	<StructureSection load='2f5n' size='340' side='right'caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2f5n' size='340' side='right'caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5N 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=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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]~~</~~div~~><~~/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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23]~~ </~~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=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [https://pdbe.org/2f5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [https://www.ebi.ac.uk/pdbsum/2f5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5n ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [https://pdbe.org/2f5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [https://www.ebi.ac.uk/pdbsum/2f5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] 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 purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]	+	[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE] 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 purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980]]~~	+	[[Category: Geobacillus stearothermophilus]]
-	~~[[Category: DNA-formamidopyrimidine glycosylase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Banerjee, A]]	+	[[Category: Banerjee A]]
-	[[Category: Santos~~, W L~~]]	+	[[Category: Santos WL]]
-	[[Category: Verdine~~, G L]]~~	+	[[Category: Verdine GL]]
-	~~[[Category: Damage search]]~~	+
-	~~[[Category: Disulfide crosslink]]~~	+
-	~~[[Category: Dna glycosylase]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 17:22, 20 October 2021

2021-10-20T17:22:31Z

←Older revision		Revision as of 17:22, 20 October 2021
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	<StructureSection load='2f5n' size='340' side='right'caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2f5n' size='340' side='right'caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2F5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5N 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=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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [~~http~~://pdbe.org/2f5n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2f5n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5n ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [https://pdbe.org/2f5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [https://www.ebi.ac.uk/pdbsum/2f5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] 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 purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]	+	[[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] 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 purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:46, 18 March 2020

2020-03-18T10:46:08Z

←Older revision		Revision as of 10:46, 18 March 2020
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	==MutM crosslinked to undamaged DNA sampling A:T base pair IC1==		==MutM crosslinked to undamaged DNA sampling A:T base pair IC1==
-	<StructureSection load='2f5n' size='340' side='right' caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2f5n' size='340' side='right'caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F5N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F5N FirstGlance]. <br>
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
		+	[[Category: Large Structures]]
	[[Category: Banerjee, A]]		[[Category: Banerjee, A]]
	[[Category: Santos, W L]]		[[Category: Santos, W L]]

OCA at 09:11, 14 June 2018

2018-06-14T09:11:14Z

←Older revision		Revision as of 09:11, 14 June 2018
Line 1:		Line 1:
		+
	==MutM crosslinked to undamaged DNA sampling A:T base pair IC1==		==MutM crosslinked to undamaged DNA sampling A:T base pair IC1==
	<StructureSection load='2f5n' size='340' side='right' caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2f5n' size='340' side='right' caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [http://pdbe.org/2f5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [http://www.ebi.ac.uk/pdbsum/2f5n 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=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [http://pdbe.org/2f5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [http://www.ebi.ac.uk/pdbsum/2f5n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/2f5n_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/2f5n_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>

OCA at 06:47, 10 February 2016

2016-02-10T06:47:39Z

←Older revision		Revision as of 06:47, 10 February 2016
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [http://www.ebi.ac.uk/pdbsum/2f5n 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=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [http://pdbe.org/2f5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [http://www.ebi.ac.uk/pdbsum/2f5n PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=2f5n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2f5n" style="background-color:#fffaf0;"></div>

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

OCA at 08:28, 8 July 2015

2015-07-08T08:28:12Z

←Older revision		Revision as of 08:28, 8 July 2015
Line 2:		Line 2:
	<StructureSection load='2f5n' size='340' side='right' caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2f5n' size='340' side='right' caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F5N 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=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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>
Line 9:		Line 9:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~P84131_BACST P84131_BACST~~]] 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 purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:~~SAAS015886_004_120556~~]	+	[[http://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] 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 purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
-	[[Category: Geobacillus stearothermophilus]]
	[[Category: Banerjee, A]]		[[Category: Banerjee, A]]
	[[Category: Santos, W L]]		[[Category: Santos, W L]]

OCA at 12:32, 25 December 2014

2014-12-25T12:32:30Z

←Older revision		Revision as of 12:32, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F5N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F5N 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=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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></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=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [http://www.ebi.ac.uk/pdbsum/2f5n 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=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [http://www.ebi.ac.uk/pdbsum/2f5n PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/P84131_BACST P84131_BACST]] 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 purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS015886_004_120556]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Banerjee, A.]]	+	[[Category: Banerjee, A]]
-	[[Category: Santos, W L.]]	+	[[Category: Santos, W L]]
-	[[Category: Verdine, G L.]]	+	[[Category: Verdine, G L]]
	[[Category: Damage search]]		[[Category: Damage search]]
	[[Category: Disulfide crosslink]]		[[Category: Disulfide crosslink]]

OCA at 09:31, 3 October 2014

2014-10-03T09:31:00Z

←Older revision		Revision as of 09:31, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2f5n.~~png~~\|~~left~~\|200px]]	+	==MutM crosslinked to undamaged DNA sampling A:T base pair IC1==
		+	<StructureSection load='2f5n' size='340' side='right' caption='[[2f5n]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F5N 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=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f5o\|2f5o]], [[2f5p\|2f5p]], [[2f5q\|2f5q]], [[2f5s\|2f5s]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></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=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [http://www.ebi.ac.uk/pdbsum/2f5n 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/f5/2f5n_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 ==
		+	DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.

-	~~{{STRUCTURE_2f5n\| PDB=2f5n \| SCENE= }}~~	+	Structure of a DNA glycosylase searching for lesions.,Banerjee A, Santos WL, Verdine GL Science. 2006 Feb 24;311(5764):1153-7. PMID:16497933<ref>PMID:16497933</ref>

-	~~===MutM crosslinked to undamaged DNA sampling A:T base pair IC1===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16497933}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2f5n]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA].~~	+

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016497933<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]

OCA at 16:42, 20 October 2012

2012-10-20T16:42:25Z

←Older revision		Revision as of 16:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2f5n]] is a 3 chain structure ~~of [[DNA glycosylate]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA].	+	[[2f5n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA].

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

OCA: Protected "2f5n" [edit=sysop:move=sysop]

2012-07-26T22:35:00Z

Protected "2f5n" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:35, 26 July 2012