7s9k | pdb_00007s9k
Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dA
Structural highlights
Function[DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.[1] [2] [3] [4] Publication Abstract from PubMedN6-(2-Deoxy-alpha,beta-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamid o pyrimidine (Fapy*dG) is a prevalent form of genomic DNA damage. Fapy*dG is formed in greater amounts under anoxic conditions than the well-studied, chemically related 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodGuo). Fapy*dG is more mutagenic in mammalian cells than 8-oxodGuo. A distinctive property of Fapy*dG is facile epimerization, but prior works with Fapy*dG analogues have precluded determining its effect on chemistry. We present crystallographic characterization of natural Fapy*dG in duplex DNA and as the template base for DNA polymerase beta (Pol beta). Fapy*dG adopts the beta-anomer when base paired with cytosine but exists as a mixture of alpha- and beta-anomers when promutagenically base paired with adenine. Rotation about the bond between the glycosidic nitrogen atom and the pyrimidine ring is also affected by the opposing nucleotide. Sodium cyanoborohydride soaking experiments trap the ring-opened Fapy*dG, demonstrating that ring opening and epimerization occur in the crystalline state. Ring opening and epimerization are facilitated by propitious water molecules that are observed in the structures. Determination of Fapy*dG mutagenicity in wild type and Pol beta knockdown HEK 293T cells indicates that Pol beta contributes to G --> T transversions but also suppresses G --> A transitions. Complementary kinetic studies have determined that Fapy*dG promotes mutagenesis by decreasing the catalytic efficiency of dCMP insertion opposite Fapy*dG, thus reducing polymerase fidelity. Kinetic studies have determined that dCMP incorporation opposite the beta-anomer is approximately 90 times faster than the alpha-anomer. This research identifies the importance of anomer dynamics, a feature unique to formamidopyrimidines, when considering the incorporation of nucleotides opposite Fapy*dG and potentially the repair of this structurally unusual lesion. Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication.,Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD J Am Chem Soc. 2022 May 11;144(18):8054-8065. doi: 10.1021/jacs.2c00193. Epub, 2022 May 2. PMID:35499923[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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