5eoz: Difference between revisions

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New page: '''Unreleased structure''' The entry 5eoz is ON HOLD until Paper Publication Authors: Koag, M.C., Lee, S Description: Mutagenicity of 7-Benzyl guanine lesion and Replication by Human D...
 
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'''Unreleased structure'''


The entry 5eoz is ON HOLD  until Paper Publication
==Mutagenicity of 7-Benzyl guanine lesion and Replication by Human DNA Polymerase beta==
<StructureSection load='5eoz' size='340' side='right'caption='[[5eoz]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5eoz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EOZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.088&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=5eoz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eoz OCA], [https://pdbe.org/5eoz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eoz RCSB], [https://www.ebi.ac.uk/pdbsum/5eoz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eoz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A wide variety of endogenous and exogenous alkylating agents attack DNA to preferentially generate N7-alkylguanine (N7-alkylG) adducts. Studies on the effect of N7-alkylG lesions on biological processes have been difficult due in part to complications arising from the chemical lability of the positively charged N7-alkylG, which can readily produce secondary lesions. To assess the effect of bulky N7-alkylG on DNA replication, we prepared chemically stable N7-benzylguanine(N7bnG)-containing DNA and evaluated nucleotide incorporation opposite the lesion by human DNA polymerase beta (polbeta), a model enzyme for high-fidelity DNA polymerases. Kinetic studies showed that the N7-benzyl-G lesion greatly inhibited dCTP incorporation by polbeta. The crystal structure of polbeta incorporating dCTP opposite N7bnG showed a Watson-Crick N7bnG:dCTP. The polbeta-N7bnG:dCTP structure showed an open protein conformation, a relatively disordered dCTP, and lack of catalytic metal, which explained the inefficient nucleotide incorporation opposite N7bnG. This indicates that polbeta is sensitive to major groove adducts in the templating-base side and deters nucleotide incorporation opposite bulky N7-alkylG adducts by adopting a catalytically incompetent conformation. Substituting Mg2+ for Mn2+ induced an open-to-closed conformational change due to the presence of catalytic metal and stably bound dCTP and increased the catalytic efficiency by ~10-fold, highlighting the effect of binding of incoming nucleotide and catalytic metal on protein not conformation and nucleotidyl transfer reaction. Overall, these results suggest that, although bulky alkyl groups at guanine-N7 may not alter base-pairing properties of guanine, the major-groove-positioned lesions in the template could impede nucleotidyl transfer by some DNA polymerases.


Authors: Koag, M.C., Lee, S
Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication.,Kou Y, Koag MC, Lee S Biochemistry. 2018 Jun 29. doi: 10.1021/acs.biochem.8b00331. PMID:29957995<ref>PMID:29957995</ref>


Description: Mutagenicity of 7-Benzyl guanine lesion and Replication by Human DNA Polymerase beta
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Koag, M.C]]
<div class="pdbe-citations 5eoz" style="background-color:#fffaf0;"></div>
[[Category: Lee, S]]
 
==See Also==
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Koag MC]]
[[Category: Lee S]]
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