3k5l

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{{Seed}}
 
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[[Image:3k5l.jpg|left|200px]]
 
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==Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) ternary complex==
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The line below this paragraph, containing "STRUCTURE_3k5l", creates the "Structure Box" on the page.
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<StructureSection load='3k5l' size='340' side='right'caption='[[3k5l]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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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'>[[3k5l]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K5L FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.7&#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=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_3k5l| PDB=3k5l | 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=3k5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5l OCA], [https://pdbe.org/3k5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k5l RCSB], [https://www.ebi.ac.uk/pdbsum/3k5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k5l ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO2_ECOLI DPO2_ECOLI] Thought to be involved in DNA repair and/or mutagenesis.
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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/k5/3k5l_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=3k5l 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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E. coli DNA Pol II and eukaryotic Rev3 are B-family polymerases that can extend primers past a damaged or mismatched site when the high-fidelity replicative polymerases in the same family are ineffective. We report here the biochemical and structural properties of DNA Pol II that facilitate this translesion synthesis. DNA Pol II can extend primers past lesions either directly or by template skipping, in which small protein cavities outside of the active site accommodate looped-out template nucleotides 1 or 2 bp upstream. Because of multiple looping-out alternatives, mutation spectra of bypass synthesis are complicated. Moreover, translesion synthesis is enhanced by altered partitioning of DNA substrate between the polymerase active site and the proofreading exonuclease site. Compared to the replicative B family polymerases, DNA Pol II has subtle amino acid changes remote from the active site that allow it to replicate normal DNA with high efficiency yet conduct translesion synthesis when needed.
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===Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) ternary complex===
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Structural insight into translesion synthesis by DNA Pol II.,Wang F, Yang W Cell. 2009 Dec 24;139(7):1279-89. PMID:20064374<ref>PMID:20064374</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 3k5l" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20064374}}, 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 20064374 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20064374}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3K5L is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5L OCA].
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==Reference==
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<ref group="xtra">PMID:20064374</ref><references group="xtra"/>
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Wang, F.]]
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[[Category: Large Structures]]
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[[Category: Yang, W.]]
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[[Category: Wang F]]
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[[Category: Dna damage]]
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[[Category: Yang W]]
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[[Category: Dna repair]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed dna polymerase]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Sos response]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:40:19 2010''
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Current revision

Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) ternary complex

PDB ID 3k5l

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