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3s6i

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Current revision (09:47, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3s6i' size='340' side='right'caption='[[3s6i]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
<StructureSection load='3s6i' size='340' side='right'caption='[[3s6i]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28&#8491;</td></tr>
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<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>
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<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>
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<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>
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<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>
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<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 ==
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[[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.
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[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.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3s6i" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-3-methyladenine glycosylase II]]
 
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[[Category: Fission yeast]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Adhikary, S]]
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[[Category: Schizosaccharomyces pombe 972h-]]
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[[Category: Eichman, B F]]
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[[Category: Adhikary S]]
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[[Category: Abasic site]]
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[[Category: Eichman BF]]
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[[Category: Dna glycosylase]]
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[[Category: Dna repair]]
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[[Category: Hydrolase-dna complex]]
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Current revision

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

PDB ID 3s6i

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