View source for 9fmf


==KlenTaq DNA polymerase in a ternary complex with primer/template and a fluorobenzofuran-modified dUTP (FBFdUTP)==
<StructureSection load='9fmf' size='340' side='right'caption='[[9fmf]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9fmf]] 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=9FMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9FMF FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1IDW:[[(2~{R},3~{S},5~{R})-5-[5-(5-fluoranyl-1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>A1IDW</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=9fmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9fmf OCA], [https://pdbe.org/9fmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9fmf RCSB], [https://www.ebi.ac.uk/pdbsum/9fmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9fmf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPO1T_THET8 DPO1T_THET8] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[UniProtKB:P52026]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Functionalizing nucleic acids using DNA polymerases is essential in biophysical and biotechnology applications. This study focuses on understanding how DNA polymerases recognize and incorporate nucleotides with diverse chemical modifications, aiming to develop advanced nucleotide probes. We present the crystal structures of ternary complexes of Thermus aquaticus DNA polymerase (KlenTaq) with C5-heterocycle-modified environment-sensitive 2'-deoxyuridine-5'-triphosphate (dUTP) probes. These nucleotides include SedUTP, BFdUTP and FBFdUTP, which bear selenophene, benzofuran and fluorobenzofuran, respectively, at the C5 position of uracil, and exhibit high conformational sensitivity. SedUTP and FBFdUTP serve as dual-app probes, combining a fluorophore with X-ray anomalous scattering Se or (19)F NMR labels. Our study reveals that the size of the heterocycle influences how DNA polymerase families A and B incorporate these modified nucleotides during single nucleotide incorporation and primer extension reactions. Remarkably, the responsiveness of FBFdUTP enabled real-time monitoring of the binary complex formation and polymerase activity through fluorescence and (19)F NMR spectroscopy. Comparative analysis of incorporation profiles, fluorescence, (19)F NMR data, and crystal structures of ternary complexes highlights the plasticity of the enzyme. Key insight is provided into the role of gatekeeper amino acids (Arg660 and Arg587) in accommodating and processing these modified substrates, offering a structural basis for next-generation nucleotide probe development.

Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes.,Ghosh P, Betz K, Gutfreund C, Pal A, Marx A, Srivatsan SG Angew Chem Int Ed Engl. 2025 Jan 10;64(2):e202414319. doi: , 10.1002/anie.202414319. Epub 2024 Nov 22. PMID:39428682<ref>PMID:39428682</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9fmf" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Thermus aquaticus]]
[[Category: Betz K]]
[[Category: Srivatsan SG]]