2M2W
Ternary complex of ASFV Pol X with DNA and MgdGTP
Summary for 2M2W
| Entry DOI | 10.2210/pdb2m2w/pdb |
| Related | 2M2T 2M2U 2M2V |
| NMR Information | BMRB: 18935 |
| Descriptor | Repair DNA polymerase X, 5'-D(P*GP*GP*CP*GP*AP*AP*GP*CP*CP*GP*GP*GP*TP*GP*CP*GP*AP*AP*GP*CP*AP*CP*(DOC))-3', 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, ... (4 entities in total) |
| Functional Keywords | dna polymerase, asfv pol x, nucleotidyl transferase, transferase-dna complex, transferase/dna |
| Biological source | African swine fever virus |
| Total number of polymer chains | 2 |
| Total formula weight | 28032.88 |
| Authors | |
| Primary citation | Wu, W.J.,Su, M.I.,Wu, J.L.,Kumar, S.,Lim, L.H.,Wang, C.W.,Nelissen, F.H.,Chen, M.C.,Doreleijers, J.F.,Wijmenga, S.S.,Tsai, M.D. How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation. J.Am.Chem.Soc., 136:4927-4937, 2014 Cited by PubMed Abstract: 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 αE, 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. PubMed: 24617852DOI: 10.1021/ja4102375 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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