2c2e

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{{Seed}}
 
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[[Image:2c2e.png|left|200px]]
 
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==Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
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The line below this paragraph, containing "STRUCTURE_2c2e", creates the "Structure Box" on the page.
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<StructureSection load='2c2e' size='340' side='right'caption='[[2c2e]], [[Resolution|resolution]] 2.61&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'>[[2c2e]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2E 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]] 2.61&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
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{{STRUCTURE_2c2e| PDB=2c2e | 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=2c2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2e OCA], [https://pdbe.org/2c2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2e RCSB], [https://www.ebi.ac.uk/pdbsum/2c2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2e ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
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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/c2/2c2e_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=2c2e 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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DNA polymerases insert dATP opposite the oxidative damage product 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) instead of dCTP, to the extent of &gt;90% with some polymerases. Steady-state kinetics with the Y-family Sulfolobus solfataricus DNA polymerase IV (Dpo4) showed 90-fold higher incorporation efficiency of dCTP &gt; dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) was similar for G and 8-oxoG templates. Mass spectral analysis of extended DNA primers showed &gt;/=95% incorporation of dCTP &gt; dATP opposite 8-oxoG. Pre-steady-state kinetics showed faster rates of dCTP incorporation opposite 8-oxoG than G. The measured K(d)(,dCTP) was 15-fold lower for an oligonucleotide containing 8-oxoG than with G. Extension beyond an 8-oxoG:C pair was similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. The E(a) for dCTP insertion opposite 8-oxoG was lower than for opposite G. Crystal structures of Dpo4 complexes with oligonucleotides were solved with C, A, and G nucleoside triphosphates placed opposite 8-oxoG. With ddCTP, dCTP, and dATP the phosphodiester bonds were formed even in the presence of Ca(2+). The 8-oxoG:C pair showed classic Watson-Crick geometry; the 8-oxoG:A pair was in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5' C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshift event observed in the catalytic assays.
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===EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8-OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4===
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Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4.,Zang H, Irimia A, Choi JY, Angel KC, Loukachevitch LV, Egli M, Guengerich FP J Biol Chem. 2006 Jan 27;281(4):2358-72. Epub 2005 Nov 22. PMID:16306039<ref>PMID:16306039</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 2c2e" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16306039}}, 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 16306039 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16306039}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2C2E is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2E OCA].
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[[Category: Saccharolobus solfataricus P2]]
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[[Category: Egli M]]
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==Reference==
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[[Category: Irimia A]]
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<ref group="xtra">PMID:16306039</ref><references group="xtra"/>
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[[Category: Loukachevitch LV]]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Sulfolobus solfataricus]]
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[[Category: Egli, M.]]
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[[Category: Irimia, A.]]
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[[Category: Loukachevitch, L V.]]
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[[Category: 8-dihydro-8-oxodeoxyguanosine]]
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[[Category: Calcium]]
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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- 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: P2 dna polymerase iv]]
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[[Category: Polymerase]]
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[[Category: Transferase]]
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[[Category: Translesion dna polymerase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:27:28 2009''
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Current revision

Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

PDB ID 2c2e

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