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4f4k

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==DNA Polymerase I Large Fragment Complex 6==
==DNA Polymerase I Large Fragment Complex 6==
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<StructureSection load='4f4k' size='340' side='right' caption='[[4f4k]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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<StructureSection load='4f4k' size='340' side='right'caption='[[4f4k]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4f4k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F4K FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4f4k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426] 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=4F4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F4K FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
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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=4f4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f4k OCA], [https://pdbe.org/4f4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f4k RCSB], [https://www.ebi.ac.uk/pdbsum/4f4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f4k ProSAT]</span></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ez6|4ez6]], [[4f2r|4f2r]], [[4f2s|4f2s]], [[4ez9|4ez9]], [[4f3o|4f3o]], [[4f8r|4f8r]]</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4f4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f4k OCA], [http://pdbe.org/4f4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f4k RCSB], [http://www.ebi.ac.uk/pdbsum/4f4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f4k ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]
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Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C*A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.
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Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.,Wang W, Hellinga HW, Beese LS Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17644-8. Epub 2011 Oct 17. PMID:22006298<ref>PMID:22006298</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 4f4k" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[DNA polymerase|DNA polymerase]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Geobacillus kaustophilus HTA426]]
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[[Category: Geoka]]
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[[Category: Large Structures]]
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[[Category: Beese, L S]]
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[[Category: Synthetic construct]]
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[[Category: Wang, W]]
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[[Category: Beese LS]]
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[[Category: Closed form]]
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[[Category: Wang W]]
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[[Category: Dna polymerase i]]
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[[Category: Protein-dna complex]]
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[[Category: Transferase-dna complex]]
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Revision as of 04:34, 7 October 2022

DNA Polymerase I Large Fragment Complex 6

PDB ID 4f4k

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