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4dfj

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==Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(aminopentinyl)-dTTP==
==Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(aminopentinyl)-dTTP==
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<StructureSection load='4dfj' size='340' side='right' caption='[[4dfj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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<StructureSection load='4dfj' size='340' side='right'caption='[[4dfj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4dfj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DFJ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4dfj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DFJ 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=0KL:5-(5-AMINOPENT-1-YN-1-YL)-2-DEOXYURIDINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>0KL</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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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]] 1.9&#8491;</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></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=0KL:5-(5-AMINOPENT-1-YN-1-YL)-2-DEOXYURIDINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>0KL</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ktq|3ktq]], [[3oju|3oju]], [[3ojs|3ojs]], [[3lwm|3lwm]], [[3lwl|3lwl]], [[3m8s|3m8s]]</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=4dfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfj OCA], [https://pdbe.org/4dfj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dfj RCSB], [https://www.ebi.ac.uk/pdbsum/4dfj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfj ProSAT]</span></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</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=4dfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dfj RCSB], [http://www.ebi.ac.uk/pdbsum/4dfj PDBsum]</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 capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.
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Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.,Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A J Am Chem Soc. 2012 Apr 11. PMID:22475415<ref>PMID:22475415</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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==See Also==
==See Also==
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*[[DNA polymerase|DNA polymerase]]
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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: DNA-directed DNA polymerase]]
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[[Category: Large Structures]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
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[[Category: Baccaro, A]]
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[[Category: Baccaro A]]
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[[Category: Bergen, K]]
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[[Category: Bergen K]]
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[[Category: Diederichs, K]]
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[[Category: Diederichs K]]
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[[Category: Marx, A]]
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[[Category: Marx A]]
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[[Category: Steck, A]]
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[[Category: Steck A]]
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[[Category: Struett, S]]
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[[Category: Struett S]]
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[[Category: Welte, W]]
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[[Category: Welte W]]
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[[Category: Dna polymerase]]
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[[Category: Transferase-dna complex]]
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Current revision

Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(aminopentinyl)-dTTP

PDB ID 4dfj

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