1xc8 - Revision history

OCA at 06:43, 23 August 2023

2023-08-23T06:43:46Z

←Older revision		Revision as of 06:43, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1xc8' size='340' side='right'caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1xc8' size='340' side='right'caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XC8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_cremoris Lactococcus cremoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XC8 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]] 1.95Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene>, <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"><div style='overflow: auto; max-height: 3em;~~'>~~[[1tdz\|1tdz]]~~</~~div></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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [https://pdbe.org/1xc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [https://www.ebi.ac.uk/pdbsum/1xc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xc8 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat"~~>~~mutm~~, ~~fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 "Streptococcus hollandicus" Scholl 1891])~~<~~/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~~://proteopedia.org/fgij/fg.htm?mol=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [~~http~~://pdbe.org/1xc8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xc8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xc8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FPG_LACLC FPG_LACLC]] 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.<ref>PMID:7704272</ref>	+	[https://www.uniprot.org/uniprot/FPG_LACLC FPG_LACLC] 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.<ref>PMID:7704272</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]]		*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
-	*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)\|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]
-	*[[Fpg Nei Protein Family\|Fpg Nei Protein Family]]
-	*[[Fpg Nei Protein Superfamily\|Fpg Nei Protein Superfamily]]
-	*[[User:Ramiro Barrantes/FpgNeiRepair\|User:Ramiro Barrantes/FpgNeiRepair]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptococcus hollandicus scholl 1891]]~~	+	[[Category: Lactococcus cremoris]]
-	~~[[Category: DNA-formamidopyrimidine glycosylase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boiteux, S]]	+	[[Category: Boiteux S]]
-	[[Category: Carell, T]]	+	[[Category: Carell T]]
-	[[Category: Castaing, B]]	+	[[Category: Castaing B]]
-	[[Category: Coste, F]]	+	[[Category: Coste F]]
-	[[Category: Ober, M]]	+	[[Category: Ober M]]
-	[[Category: Zelwer, C]]	+	[[Category: Zelwer C]]
-	~~[[Category: Fapy]]~~	+
-	~~[[Category: Glycosylase]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 09:52, 6 January 2021

2021-01-06T09:52:51Z

←Older revision		Revision as of 09:52, 6 January 2021
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	==CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA==		==CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA==
-	<StructureSection load='1xc8' size='340' side='right' caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='1xc8' size='340' side='right'caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XC8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XC8 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tdz\|1tdz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tdz\|1tdz]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 "Streptococcus hollandicus" Scholl 1891])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 "Streptococcus hollandicus" Scholl 1891])</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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://pdbe.org/1xc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xc8 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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://pdbe.org/1xc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xc8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 34:		Line 34:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)\|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]		*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)\|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]
	*[[Fpg Nei Protein Family\|Fpg Nei Protein Family]]		*[[Fpg Nei Protein Family\|Fpg Nei Protein Family]]
	*[[Fpg Nei Protein Superfamily\|Fpg Nei Protein Superfamily]]		*[[Fpg Nei Protein Superfamily\|Fpg Nei Protein Superfamily]]
		+	*[[User:Ramiro Barrantes/FpgNeiRepair\|User:Ramiro Barrantes/FpgNeiRepair]]
	== References ==		== References ==
	<references/>		<references/>
Line 44:		Line 45:
	[[Category: Streptococcus hollandicus scholl 1891]]		[[Category: Streptococcus hollandicus scholl 1891]]
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
		+	[[Category: Large Structures]]
	[[Category: Boiteux, S]]		[[Category: Boiteux, S]]
	[[Category: Carell, T]]		[[Category: Carell, T]]

OCA at 07:17, 18 April 2018

2018-04-18T07:17:47Z

←Older revision		Revision as of 07:17, 18 April 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA==		==CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA==
	<StructureSection load='1xc8' size='340' side='right' caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1xc8' size='340' side='right' caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 "Streptococcus hollandicus" Scholl 1891])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 "Streptococcus hollandicus" Scholl 1891])</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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://pdbe.org/1xc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://pdbe.org/1xc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xc8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xc/1xc8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xc/1xc8_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 13:26, 9 February 2016

2016-02-09T13:26:03Z

←Older revision		Revision as of 13:26, 9 February 2016
Line 20:		Line 20:
	<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=1xc8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:40, 10 September 2015

2015-09-10T22:40:29Z

←Older revision		Revision as of 22:40, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1xc8' size='340' side='right' caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1xc8' size='340' side='right' caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Lactococcus_lactis_subsp._cremoris Lactococcus lactis subsp. cremoris~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XC8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XC8 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tdz\|1tdz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tdz\|1tdz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 ~~Lactococcus lactis subsp. cremoris~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 "Streptococcus hollandicus" Scholl 1891])</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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://pdbe.org/1xc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	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 1xc8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 40:		Line 41:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptococcus hollandicus scholl 1891]]
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
-	[[Category: Lactococcus lactis subsp. cremoris]]
	[[Category: Boiteux, S]]		[[Category: Boiteux, S]]
	[[Category: Carell, T]]		[[Category: Carell, T]]

OCA at 07:05, 25 December 2014

2014-12-25T07:05:25Z

←Older revision		Revision as of 07:05, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris Lactococcus lactis subsp. cremoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XC8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris Lactococcus lactis subsp. cremoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XC8 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>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tdz\|1tdz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tdz\|1tdz]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 Lactococcus lactis subsp. cremoris])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 Lactococcus lactis subsp. cremoris])</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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FPG_LACLC FPG_LACLC]] 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.<ref>PMID:7704272</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 40:		Line 42:
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
	[[Category: Lactococcus lactis subsp. cremoris]]		[[Category: Lactococcus lactis subsp. cremoris]]
-	[[Category: Boiteux, S.]]	+	[[Category: Boiteux, S]]
-	[[Category: Carell, T.]]	+	[[Category: Carell, T]]
-	[[Category: Castaing, B.]]	+	[[Category: Castaing, B]]
-	[[Category: Coste, F.]]	+	[[Category: Coste, F]]
-	[[Category: Ober, M.]]	+	[[Category: Ober, M]]
-	[[Category: Zelwer, C.]]	+	[[Category: Zelwer, C]]
	[[Category: Fapy]]		[[Category: Fapy]]
	[[Category: Glycosylase]]		[[Category: Glycosylase]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

OCA at 08:32, 3 October 2014

2014-10-03T08:32:26Z

←Older revision		Revision as of 08:32, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1xc8\| PDB=1xc8 \| SCENE= }}~~	+	==CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA==
-	===CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA===	+	<StructureSection load='1xc8' size='340' side='right' caption='[[1xc8]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	{~~{ABSTRACT_PUBMED_15249553}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris Lactococcus lactis subsp. cremoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XC8 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>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tdz\|1tdz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutm, fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1359 Lactococcus lactis subsp. cremoris])</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=1xc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xc8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xc8 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/xc/1xc8_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 ==
		+	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines such as 7,8-dihydro-8-oxoguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) from damaged DNA. Here, we report the crystal structure of the Fpg protein from Lactococcus lactis (LlFpg) bound to a carbocyclic FapydG (cFapydG)-containing DNA. The structure reveals that Fpg stabilizes the cFapydG nucleoside into an extrahelical conformation inside its substrate binding pocket. In contrast to the recognition of the 8-oxodG lesion, which is bound with the glycosidic bond in a syn conformation, the cFapydG lesion displays in the complex an anti conformation. Furthermore, Fpg establishes interactions with all the functional groups of the FapyG base lesion, which can be classified in two categories: (i) those specifying a purine-derived lesion (here a guanine) involved in the Watson-Crick face recognition of the lesion and probably contributing to an optimal orientation of the pyrimidine ring moiety in the binding pocket and (ii) those specifying the imidazole ring-opened moiety of FapyG and probably participating also in the rotameric selection of the FapydG nucleobase. These interactions involve strictly conserved Fpg residues and structural water molecules mediated interactions. The significant differences between the Fpg recognition modes of 8-oxodG and FapydG provide new insights into the Fpg substrate specificity.

-	~~==About this Structure==~~	+	Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase.,Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B J Biol Chem. 2004 Oct 15;279(42):44074-83. Epub 2004 Jul 10. PMID:15249553<ref>PMID:15249553</ref>
-	~~[[1xc8]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Lactococcus_lactis_subsp~~.~~_cremoris Lactococcus lactis subsp~~. ~~cremoris]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1XC8 OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
	*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)\|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]		*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)\|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]
	*[[Fpg Nei Protein Family\|Fpg Nei Protein Family]]		*[[Fpg Nei Protein Family\|Fpg Nei Protein Family]]
	*[[Fpg Nei Protein Superfamily\|Fpg Nei Protein Superfamily]]		*[[Fpg Nei Protein Superfamily\|Fpg Nei Protein Superfamily]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015249553<~~/~~ref~~><~~ref group="xtra">PMID:018635007</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-formamidopyrimidine glycosylase]]		[[Category: DNA-formamidopyrimidine glycosylase]]
	[[Category: Lactococcus lactis subsp. cremoris]]		[[Category: Lactococcus lactis subsp. cremoris]]

OCA at 09:21, 11 March 2013

2013-03-11T09:21:53Z

←Older revision		Revision as of 09:21, 11 March 2013
Line 1:		Line 1:
-	[[Image:1xc8.png\|left\|200px]]
-
	{{STRUCTURE_1xc8\| PDB=1xc8 \| SCENE= }}		{{STRUCTURE_1xc8\| PDB=1xc8 \| SCENE= }}
-
	===CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA===		===CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA===
-
	{{ABSTRACT_PUBMED_15249553}}		{{ABSTRACT_PUBMED_15249553}}

OCA at 13:59, 20 October 2012

2012-10-20T13:59:20Z

←Older revision		Revision as of 13:59, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1xc8]] is a 3 chain structure ~~of [[DNA glycosylate]]~~ with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris Lactococcus lactis subsp. cremoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA].	+	[[1xc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris Lactococcus lactis subsp. cremoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XC8 OCA].

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

OCA: Protected "1xc8" [edit=sysop:move=sysop]

2012-07-26T13:42:54Z

Protected "1xc8" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:42, 26 July 2012