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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==
<StructureSection load='4dfj' size='340' side='right' caption='[[4dfj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='4dfj' size='340' side='right'caption='[[4dfj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4dfj]] 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=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>
<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>
</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>
</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>
<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>
<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>
<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>
<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>
<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 ATCC 25104])</td></tr>
<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>
<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://pdbe.org/4dfj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dfj RCSB], [http://www.ebi.ac.uk/pdbsum/4dfj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfj ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4dfj" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[DNA polymerase|DNA polymerase]]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 25104]]
[[Category: Large Structures]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Thermus aquaticus]]
[[Category: Baccaro, A]]
[[Category: Baccaro A]]
[[Category: Bergen, K]]
[[Category: Bergen K]]
[[Category: Diederichs, K]]
[[Category: Diederichs K]]
[[Category: Marx, A]]
[[Category: Marx A]]
[[Category: Steck, A]]
[[Category: Steck A]]
[[Category: Struett, S]]
[[Category: Struett S]]
[[Category: Welte, W]]
[[Category: Welte W]]
[[Category: Dna polymerase]]
[[Category: Transferase-dna complex]]

Latest revision as of 17:34, 14 March 2024

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

Structural highlights

4dfj is a 3 chain structure with sequence from Thermus aquaticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO1_THEAQ

See Also

4dfj, resolution 1.90Å

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