3in5

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{{Seed}}
 
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[[Image:3in5.jpg|left|200px]]
 
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==Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion==
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The line below this paragraph, containing "STRUCTURE_3in5", creates the "Structure Box" on the page.
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<StructureSection load='3in5' size='340' side='right'caption='[[3in5]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3in5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3hed 3hed]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IN5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IN5 FirstGlance]. <br>
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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]] 3.2&#8491;</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=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_3in5| PDB=3in5 | SCENE= }}
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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=3in5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3in5 OCA], [https://pdbe.org/3in5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3in5 RCSB], [https://www.ebi.ac.uk/pdbsum/3in5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3in5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/POLK_HUMAN POLK_HUMAN] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.<ref>PMID:10620008</ref> <ref>PMID:11024016</ref> <ref>PMID:12145297</ref> <ref>PMID:12444249</ref> <ref>PMID:12952891</ref> <ref>PMID:14630940</ref> <ref>PMID:15533436</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/in/3in5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3in5 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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BACKGROUND: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase kappa (Polkappa) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polkappa's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polkappa in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide. METHODOLOGY AND PRINCIPAL FINDINGS: We show that the Polkappa active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP. CONCLUSIONS AND SIGNIFICANCE: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polkappa is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polkappa is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.
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===Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion===
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Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion.,Vasquez-Del Carpio R, Silverstein TD, Lone S, Swan MK, Choudhury JR, Johnson RE, Prakash S, Prakash L, Aggarwal AK PLoS One. 2009 Jun 2;4(6):e5766. PMID:19492058<ref>PMID:19492058</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 3in5" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19492058}}, adds the Publication Abstract to the page
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19492058 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19492058}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3IN5 is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3hed 3hed]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IN5 OCA].
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==Reference==
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<ref group="xtra">PMID:19492058</ref><references group="xtra"/>
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Aggarwal, A K.]]
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[[Category: Large Structures]]
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[[Category: Carpio, R Vasquez-Del.]]
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[[Category: Aggarwal AK]]
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[[Category: Silverstein, T D.]]
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[[Category: Silverstein TD]]
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[[Category: Alternative splicing]]
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[[Category: Vasquez-Del Carpio R]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Dna replication]]
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[[Category: Dna synthesis]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed dna polymerase]]
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[[Category: Magnesium]]
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[[Category: Metal-binding]]
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[[Category: Mutator protein]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Polymorphism]]
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[[Category: Schiff base]]
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[[Category: Transferase]]
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[[Category: Transferase/dna complex]]
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[[Category: Zinc]]
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[[Category: Zinc-finger]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 09:16:26 2009''
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Current revision

Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion

PDB ID 3in5

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