| 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 PubMed
N6-(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
- ↑ Bennett RA, Wilson DM 3rd, Wong D, Demple B. Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7166-9. PMID:9207062
- ↑ Matsumoto Y, Kim K, Katz DS, Feng JA. Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups. Biochemistry. 1998 May 5;37(18):6456-64. PMID:9572863 doi:10.1021/bi9727545
- ↑ DeMott MS, Beyret E, Wong D, Bales BC, Hwang JT, Greenberg MM, Demple B. Covalent trapping of human DNA polymerase beta by the oxidative DNA lesion 2-deoxyribonolactone. J Biol Chem. 2002 Mar 8;277(10):7637-40. Epub 2002 Jan 22. PMID:11805079 doi:10.1074/jbc.C100577200
- ↑ Parsons JL, Dianova II, Khoronenkova SV, Edelmann MJ, Kessler BM, Dianov GL. USP47 is a deubiquitylating enzyme that regulates base excision repair by controlling steady-state levels of DNA polymerase beta. Mol Cell. 2011 Mar 4;41(5):609-15. doi: 10.1016/j.molcel.2011.02.016. PMID:21362556 doi:10.1016/j.molcel.2011.02.016
- ↑ Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD. Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J Am Chem Soc. 2022 May 11;144(18):8054-8065. doi: 10.1021/jacs.2c00193. Epub, 2022 May 2. PMID:35499923 doi:http://dx.doi.org/10.1021/jacs.2c00193
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