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2m2w

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==Ternary complex of ASFV Pol X with DNA and MgdGTP==
==Ternary complex of ASFV Pol X with DNA and MgdGTP==
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<StructureSection load='2m2w' size='340' side='right' caption='[[2m2w]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
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<StructureSection load='2m2w' size='340' side='right'caption='[[2m2w]]' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2m2w]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M2W FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2m2w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/African_swine_fever_virus African swine fever virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M2W 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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">Solution NMR</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</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">[[2m2t|2m2t]], [[2m2u|2m2u]], [[2m2v|2m2v]]</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=2m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2w OCA], [https://pdbe.org/2m2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m2w RCSB], [https://www.ebi.ac.uk/pdbsum/2m2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2w ProSAT]</span></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=2m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m2w RCSB], [http://www.ebi.ac.uk/pdbsum/2m2w 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/DPOLX_ASFB7 DPOLX_ASFB7] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>
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A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix alphaE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.
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How a Low-Fidelity DNA Polymerase Chooses Non-Watson-Crick from Watson-Crick Incorporation.,Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW, Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai MD J Am Chem Soc. 2014 Mar 21. PMID:24617852<ref>PMID:24617852</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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==See Also==
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</div>
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed DNA polymerase]]
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[[Category: African swine fever virus]]
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[[Category: Su, M]]
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[[Category: Large Structures]]
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[[Category: Tsai, M]]
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[[Category: Su M]]
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[[Category: Wu, W]]
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[[Category: Tsai M]]
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[[Category: Asfv pol x]]
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[[Category: Wu W]]
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[[Category: Dna polymerase]]
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[[Category: Nucleotidyl transferase]]
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[[Category: Transferase-dna complex]]
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Current revision

Ternary complex of ASFV Pol X with DNA and MgdGTP

PDB ID 2m2w

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