8ilg | pdb_00008ilg
The crystal structure of dG-DNA:Pol X product binary complex
Structural highlights
FunctionDPOLX_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.[1] [2] Publication Abstract from PubMedDNA synthesis catalyzed by DNA polymerase is essential for all life forms, and phosphodiester bond formation with phosphorus center inversion is a key step in this process. Herein, by using a single-selenium-atom-modified dNTP probe, we report a novel strategy to visualize the reaction stereochemistry and catalysis. We capture the before- and after-reaction states and provide explicit evidence of the center inversion and in-line attacking S(N)2 mechanism of DNA polymerization, while solving the diastereomer absolute configurations. Further, our kinetic and thermodynamic studies demonstrate that in the presence of Mg(2+) ions (or Mn(2+)), the binding affinity (K(m)) and reaction selectivity (k(cat)/K(m)) of dGTPalphaSe-Rp were 51.1-fold (or 19.5-fold) stronger and 21.8-fold (or 11.3-fold) higher than those of dGTPalphaSe-Sp, respectively, indicating that the diastereomeric Se-Sp atom was quite disruptive of the binding and catalysis. Our findings reveal that the third metal ion is much more critical than the other two metal ions in both substrate recognition and bond formation, providing insights into how to better design the polymerase inhibitors and discover the therapeutics. Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.,Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z Int J Mol Sci. 2023 Oct 30;24(21):15758. doi: 10.3390/ijms242115758. PMID:37958741[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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