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

Wu, W.,Su, M.,Tsai, M. (deposition date: 2013-01-03, release date: 2014-04-02, Last modification date: 2024-05-01)

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

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: 24617852
DOI: 10.1021/ja4102375

Experimental method

SOLUTION NMR