3s6i - Revision history

OCA at 09:47, 1 March 2024

2024-03-01T09:47:50Z

←Older revision		Revision as of 09:47, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3s6i' size='340' side='right'caption='[[3s6i]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='3s6i' size='340' side='right'caption='[[3s6i]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S6I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S6I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.28Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1~~, ~~SPAPB24D3.04c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21]~~ </~~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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [https://pdbe.org/3s6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [https://www.ebi.ac.uk/pdbsum/3s6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s6i 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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [https://pdbe.org/3s6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [https://www.ebi.ac.uk/pdbsum/3s6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s6i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MAG1_SCHPO MAG1_SCHPO]] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions. Can release ethylated and propylated bases from DNA in addition to 3-methyladenine.	+	[https://www.uniprot.org/uniprot/MAG1_SCHPO MAG1_SCHPO] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions. Can release ethylated and propylated bases from DNA in addition to 3-methyladenine.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N(6)-ethenoadenine (varepsilonA) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their varepsilonA activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.	+
-		+
-	Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.,Adhikary S, Eichman BF EMBO Rep. 2011 Dec 1;12(12):1286-92. doi: 10.1038/embor.2011.189. PMID:21960007<ref>PMID:21960007</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3s6i" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]		*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: DNA-3-methyladenine glycosylase II]]
-	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Adhikary, S~~]]	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	[[Category: ~~Eichman, B F~~]]	+	[[Category: Adhikary S]]
-	[[Category: ~~Abasic site]]~~	+	[[Category: Eichman BF]]
-	~~[[Category: Dna glycosylase]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 10:40, 22 June 2022

2022-06-22T10:40:16Z

←Older revision		Revision as of 10:40, 22 June 2022
Line 1:		Line 1:

	==Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.==		==Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.==
-	<StructureSection load='3s6i' size='340' side='right' caption='[[3s6i]], [[Resolution\|resolution]] 2.28Å' scene=''>	+	<StructureSection load='3s6i' size='340' side='right'caption='[[3s6i]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S6I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S6I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1, SPAPB24D3.04c ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1, SPAPB24D3.04c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </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-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [~~http~~://pdbe.org/3s6i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s6i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s6i 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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [https://pdbe.org/3s6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [https://www.ebi.ac.uk/pdbsum/3s6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s6i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MAG1_SCHPO MAG1_SCHPO]] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions. Can release ethylated and propylated bases from DNA in addition to 3-methyladenine.	+	[[https://www.uniprot.org/uniprot/MAG1_SCHPO MAG1_SCHPO]] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions. Can release ethylated and propylated bases from DNA in addition to 3-methyladenine.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 30:
	[[Category: DNA-3-methyladenine glycosylase II]]		[[Category: DNA-3-methyladenine glycosylase II]]
	[[Category: Fission yeast]]		[[Category: Fission yeast]]
		+	[[Category: Large Structures]]
	[[Category: Adhikary, S]]		[[Category: Adhikary, S]]
	[[Category: Eichman, B F]]		[[Category: Eichman, B F]]

OCA at 12:09, 11 August 2016

2016-08-11T12:09:13Z

←Older revision		Revision as of 12:09, 11 August 2016
Line 1:		Line 1:
		+
	==Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.==		==Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.==
	<StructureSection load='3s6i' size='340' side='right' caption='[[3s6i]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='3s6i' size='340' side='right' caption='[[3s6i]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Schizosaccharomyces_pombe Schizosaccharomyces pombe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S6I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S6I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1, SPAPB24D3.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~4896 Schizosaccharomyces pombe~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1, SPAPB24D3.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </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-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [http://www.ebi.ac.uk/pdbsum/3s6i 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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [http://pdbe.org/3s6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [http://www.ebi.ac.uk/pdbsum/3s6i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s6i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MAG1_SCHPO MAG1_SCHPO]] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions. Can release ethylated and propylated bases from DNA in addition to 3-methyladenine.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 20:
	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 3s6i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: DNA-3-methyladenine glycosylase II]]		[[Category: DNA-3-methyladenine glycosylase II]]
-	[[Category: ~~Schizosaccharomyces pombe~~]]	+	[[Category: Fission yeast]]
	[[Category: Adhikary, S]]		[[Category: Adhikary, S]]
	[[Category: Eichman, B F]]		[[Category: Eichman, B F]]

OCA at 10:57, 4 January 2015

2015-01-04T10:57:49Z

←Older revision		Revision as of 10:57, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S6I FirstGlance]. <br>		<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S6I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1, SPAPB24D3.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1, SPAPB24D3.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </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-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [http://www.ebi.ac.uk/pdbsum/3s6i 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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [http://www.ebi.ac.uk/pdbsum/3s6i PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 15:
	Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.,Adhikary S, Eichman BF EMBO Rep. 2011 Dec 1;12(12):1286-92. doi: 10.1038/embor.2011.189. PMID:21960007<ref>PMID:21960007</ref>		Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.,Adhikary S, Eichman BF EMBO Rep. 2011 Dec 1;12(12):1286-92. doi: 10.1038/embor.2011.189. PMID:21960007<ref>PMID:21960007</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 23:		Line 23:
	[[Category: DNA-3-methyladenine glycosylase II]]		[[Category: DNA-3-methyladenine glycosylase II]]
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
-	[[Category: Adhikary, S.]]	+	[[Category: Adhikary, S]]
-	[[Category: Eichman, B F.]]	+	[[Category: Eichman, B F]]
	[[Category: Abasic site]]		[[Category: Abasic site]]
	[[Category: Dna glycosylase]]		[[Category: Dna glycosylase]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]

OCA at 05:25, 5 June 2014

2014-06-05T05:25:21Z

←Older revision		Revision as of 05:25, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3s6i.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.==
		+	<StructureSection load='3s6i' size='340' side='right' caption='[[3s6i]], [[Resolution\|resolution]] 2.28Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s6i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S6I FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mag1, SPAPB24D3.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </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=3s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s6i RCSB], [http://www.ebi.ac.uk/pdbsum/3s6i PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N(6)-ethenoadenine (varepsilonA) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their varepsilonA activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.

-	~~<!--~~	+	Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.,Adhikary S, Eichman BF EMBO Rep. 2011 Dec 1;12(12):1286-92. doi: 10.1038/embor.2011.189. PMID:21960007<ref>PMID:21960007</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3s6i"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_3s6i\| PDB=3s6i \| SCENE= }}~~	+

-	~~===Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21960007}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21960007 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21960007}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3s6i]] is a 6 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021960007<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: DNA-3-methyladenine glycosylase II]]		[[Category: DNA-3-methyladenine glycosylase II]]
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]

OCA at 11:35, 14 December 2011

2011-12-14T11:35:43Z

←Older revision		Revision as of 11:35, 14 December 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3s6i.jpg\|left\|200px]]

-	The ~~entry 3s6i~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s6i", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3s6i\| PDB=3s6i \| SCENE= }}

-	~~Authors: Adhikary, S., Eichman, B.F~~.	+	===Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.===

-	~~Description: Schizosaccaromyces pombe 3~~-~~methyladenine DNA glycosylase~~ (~~Mag1~~) ~~in complex~~ with ~~abasic~~-DNA.	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21960007}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21960007 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21960007}}
		+
		+	==About this Structure==
		+	[[3s6i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6I OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021960007</ref><references group="xtra"/>
		+	[[Category: DNA-3-methyladenine glycosylase II]]
		+	[[Category: Schizosaccharomyces pombe]]
		+	[[Category: Adhikary, S.]]
		+	[[Category: Eichman, B F.]]
		+	[[Category: Abasic site]]
		+	[[Category: Dna glycosylase]]
		+	[[Category: Dna repair]]
		+	[[Category: Hydrolase-dna complex]]

OCA at 05:54, 15 June 2011

2011-06-15T05:54:50Z

←Older revision		Revision as of 05:54, 15 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s6i is ON HOLD	+	The entry 3s6i is ON HOLD until Paper Publication

	Authors: Adhikary, S., Eichman, B.F.		Authors: Adhikary, S., Eichman, B.F.

	Description: Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.		Description: Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.

OCA: Protected "3s6i" [edit=sysop:move=sysop]

2011-06-01T05:28:03Z

Protected "3s6i" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:28, 1 June 2011

OCA: New page: '''Unreleased structure''' The entry 3s6i is ON HOLD Authors: Adhikary, S., Eichman, B.F. Description: Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with a...

2011-06-01T05:28:02Z

New page: '''Unreleased structure''' The entry 3s6i is ON HOLD Authors: Adhikary, S., Eichman, B.F. Description: Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with a...

New page

'''Unreleased structure'''

The entry 3s6i is ON HOLD

Authors: Adhikary, S., Eichman, B.F.

Description: Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.