4b23: Difference between revisions

Latest revision as of 10:56, 9 May 2024

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

Structural highlights

4b23 is a 3 chain structure with sequence from Schizosaccharomyces pombe and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	3DR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MAG2_SCHPO Invlved in base excision repair of methyl methanesulfonate-damaged DNA by hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions.^[1]

Publication Abstract from PubMed

Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which further pass on nicked DNA to downstream DNA polymerases and ligases. The coordinated handover of cytotoxic intermediates between different BER enzymes is most likely facilitated by the DNA conformation. Here, we present the atomic structure of Schizosaccharomyces pombe Mag2 in complex with DNA to reveal an unexpected structural basis for nonenzymatic AP site recognition with an unflipped AP site. Two surface-exposed loops intercalate and widen the DNA minor groove to generate a DNA conformation previously only found in the mismatch repair MutS-DNA complex. Consequently, the molecular role of Mag2 appears to be AP site recognition and protection, while possibly facilitating damage signaling by structurally sculpting the DNA substrate.

Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2.,Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom RJ, McMurray CT, Alseth I, Tainer JA, Bjoras M Structure. 2012 Dec 11. pii: S0969-2126(12)00419-4. doi:, 10.1016/j.str.2012.11.004. PMID:23245849^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kanamitsu K, Tanihigashi H, Tanita Y, Inatani S, Ikeda S. Involvement of 3-methyladenine DNA glycosylases Mag1p and Mag2p in base excision repair of methyl methanesulfonate-damaged DNA in the fission yeast Schizosaccharomyces pombe. Genes Genet Syst. 2007 Dec;82(6):489-94. PMID:18270439
↑ Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom RJ, McMurray CT, Alseth I, Tainer JA, Bjoras M. Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2. Structure. 2012 Dec 11. pii: S0969-2126(12)00419-4. doi:, 10.1016/j.str.2012.11.004. PMID:23245849 doi:https://dx.doi.org/10.1016/j.str.2012.11.004

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kanamitsu K, Tanihigashi H, Tanita Y, Inatani S, Ikeda S. Involvement of 3-methyladenine DNA glycosylases Mag1p and Mag2p in base excision repair of methyl methanesulfonate-damaged DNA in the fission yeast Schizosaccharomyces pombe. Genes Genet Syst. 2007 Dec;82(6):489-94. PMID:18270439

[2] Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom RJ, McMurray CT, Alseth I, Tainer JA, Bjoras M. Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2. Structure. 2012 Dec 11. pii: S0969-2126(12)00419-4. doi:, 10.1016/j.str.2012.11.004. PMID:23245849 doi:https://dx.doi.org/10.1016/j.str.2012.11.004

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='4b23' size='340' side='right'caption='[[4b23]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4b23]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B23 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4b23]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B23 FirstGlance]. <br>
-</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>
+</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4b21|4b21]], [[4b22|4b22]], [[4b24|4b24]]</div></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></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=4b23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b23 OCA], [https://pdbe.org/4b23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b23 RCSB], [https://www.ebi.ac.uk/pdbsum/4b23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b23 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MAG2_SCHPO MAG2_SCHPO]] Invlved in base excision repair of methyl methanesulfonate-damaged DNA by hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions.<ref>PMID:18270439</ref>
+[https://www.uniprot.org/uniprot/MAG2_SCHPO MAG2_SCHPO] Invlved in base excision repair of methyl methanesulfonate-damaged DNA by hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine or 7-methyladenine from the damaged DNA polymer formed by alkylation lesions.<ref>PMID:18270439</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Cbs 356]]
-[[Category: DNA-3-methyladenine glycosylase II]]
 [[Category: Large Structures]]
-[[Category: Alseth, I]]
+[[Category: Schizosaccharomyces pombe]]
-[[Category: Bjoras, M]]
+[[Category: Synthetic construct]]
-[[Category: Dalhus, B]]
+[[Category: Alseth I]]
-[[Category: Forstrom, R J]]
+[[Category: Bjoras M]]
-[[Category: Huffman, J]]
+[[Category: Dalhus B]]
-[[Category: Korvald, H]]
+[[Category: Forstrom RJ]]
-[[Category: McMurray, C T]]
+[[Category: Huffman J]]
-[[Category: Nilsen, L]]
+[[Category: Korvald H]]
-[[Category: Tainer, J A]]
+[[Category: McMurray CT]]
-[[Category: Helix-hairpin-helix dna glycosylase homologue]]
+[[Category: Nilsen L]]
-[[Category: Hydrolase]]
+[[Category: Tainer JA]]
-[[Category: Hydrolase-dna complex]]

4b23: Difference between revisions

Latest revision as of 10:56, 9 May 2024

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

Structural highlights

Function

Publication Abstract from PubMed

References

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