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4c8k

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<StructureSection load='4c8k' size='340' side='right'caption='[[4c8k]], [[Resolution|resolution]] 2.17&Aring;' scene=''>
<StructureSection load='4c8k' size='340' side='right'caption='[[4c8k]], [[Resolution|resolution]] 2.17&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4c8k]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C8K FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4c8k]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] 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=4C8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C8K 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=BMR:((2R,3S,5R)-3-HYDROXY-5-(3-METHOXYNAPHTHALEN-2-YL)METHYL-TETRAHYDROGEN-TRIPHOSPHATE'>BMR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=BMR:((2R,3S,5R)-3-HYDROXY-5-(3-METHOXYNAPHTHALEN-2-YL)METHYL-TETRAHYDROGEN-TRIPHOSPHATE'>BMR</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=LHO:2-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-METHYLISOQUINOLINE-1(2H)-THIONE'>LHO</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=4c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8k OCA], [https://pdbe.org/4c8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c8k RCSB], [https://www.ebi.ac.uk/pdbsum/4c8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c8k ProSAT]</span></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4c8j|4c8j]], [[4c8l|4c8l]], [[4c8m|4c8m]], [[4c8n|4c8n]], [[4c8o|4c8o]]</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=4c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c8k OCA], [http://pdbe.org/4c8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4c8k RCSB], [http://www.ebi.ac.uk/pdbsum/4c8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4c8k 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/DPO1_THEAQ DPO1_THEAQ]]
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The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.
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Structural Insights into DNA Replication without Hydrogen Bonds.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A J Am Chem Soc. 2013 Nov 27. PMID:24283923<ref>PMID:24283923</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 4c8k" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 25104]]
 
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[[Category: DNA-directed DNA polymerase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Betz, K]]
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[[Category: Synthetic construct]]
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[[Category: Diederichs, K]]
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[[Category: Thermus aquaticus]]
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[[Category: Lavergne, T]]
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[[Category: Betz K]]
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[[Category: Malyshev, D A]]
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[[Category: Diederichs K]]
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[[Category: Marx, A]]
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[[Category: Lavergne T]]
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[[Category: Romesberg, F E]]
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[[Category: Malyshev DA]]
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[[Category: Welte, W]]
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[[Category: Marx A]]
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[[Category: Artificial nucleotide]]
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[[Category: Romesberg FE]]
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[[Category: Binary complex]]
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[[Category: Welte W]]
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[[Category: Klentaq]]
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[[Category: Transferase-dna complex]]
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[[Category: Unnatural nucleotide]]
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Revision as of 17:32, 7 September 2022

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP

PDB ID 4c8k

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