3au2

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<StructureSection load='3au2' size='340' side='right'caption='[[3au2]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='3au2' size='340' side='right'caption='[[3au2]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3au2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AU2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AU2 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3au2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AU2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AU2 FirstGlance]. <br>
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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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.4&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3au6|3au6]]</div></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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PolX, TTHA1150 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3au2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3au2 OCA], [https://pdbe.org/3au2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3au2 RCSB], [https://www.ebi.ac.uk/pdbsum/3au2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3au2 ProSAT]</span></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=3au2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3au2 OCA], [https://pdbe.org/3au2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3au2 RCSB], [https://www.ebi.ac.uk/pdbsum/3au2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3au2 ProSAT]</span></td></tr>
</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/Q5SJ64_THET8 Q5SJ64_THET8]
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DNA with single-nucleotide (1-nt) gaps can arise during various DNA processing events. These lesions are repaired by X-family DNA polymerases (PolXs) with high gap-filling activity. Some PolXs can bind productively to dNTPs in the absence of DNA and fill these 1-nt gaps. Although PolXs have a crucial role in efficient gap filling, currently, little is known of the kinetic and structural details of their productive dNTP binding. Here, we show that Thermus thermophilus HB8 PolX (ttPolX) had strong binding affinity for Mg(2+)-dNTPs in the absence of DNA and that it follows a Theorell-Chance (hit-and-run) mechanism with nucleotide binding first. Comparison of the intermediate crystal structures of ttPolX in a binary complex with dGTP and in a ternary complex with 1-nt gapped DNA and Mg(2+)-ddGTP revealed that the conformation of the incoming nucleotide depended on whether or not DNA was present. Furthermore, the Lys263 residue located between two guanosine conformations was essential to the strong binding affinity of the enzyme. The ability to bind to either syn-dNTP or anti-dNTP and the involvement of a Theorell-Chance mechanism are key aspects of the strong nucleotide-binding and efficient gap-filling activities of ttPolX.
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The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.,Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R J Mol Biol. 2012 Mar 30;417(3):179-96. Epub 2012 Jan 27. PMID:22306405<ref>PMID:22306405</ref>
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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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 3au2" style="background-color:#fffaf0;"></div>
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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]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thet8]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Ishikawa, H]]
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[[Category: Ishikawa H]]
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[[Category: Kuramitsu, S]]
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[[Category: Kuramitsu S]]
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[[Category: Masui, R]]
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[[Category: Masui R]]
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[[Category: Nakagawa, N]]
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[[Category: Nakagawa N]]
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[[Category: Nakane, S]]
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[[Category: Nakane S]]
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[[Category: Structural genomic]]
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[[Category: Wakamatsu T]]
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[[Category: Wakamatsu, T]]
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[[Category: Ap endonuclease]]
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[[Category: Dna binding]]
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[[Category: Dna polymerase]]
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[[Category: Dna repair]]
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[[Category: Drp lyase]]
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[[Category: Nucleotide binding]]
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[[Category: Php domain]]
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[[Category: Polxc doamin]]
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[[Category: Rsgi]]
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[[Category: Transferase]]
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Current revision

DNA polymerase X from Thermus thermophilus HB8 complexed with Ca-dGTP

PDB ID 3au2

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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