Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase.
Thymine DNA glycosylase (TDG) is a base excision repair enzyme with key functions in epigenetic regulation. Performing a critical step in a pathway for active DNA demethylation, TDG removes 5-formylcytosine and 5-carboxylcytosine, oxidized derivatives of 5-methylcytosine that are generated by TET (ten-eleven translocation) enzymes. We determined a crystal structure of TDG bound to DNA with a noncleavable (2'-fluoroarabino) analogue of 5-formyldeoxycytidine flipped into its active site, revealing how it recognizes and hydrolytically excises fC. Together with previous structural and biochemical findings, the results illustrate how TDG employs an adaptable active site to excise a broad variety of nucleobases from DNA.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.
Lakshmi S
LS
Pidugu
Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.
Joshua W
JW
Flowers
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.
Christopher T
CT
Coey
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.|Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research , Rockville, Maryland 20850, United States.
Edwin
E
Pozharski
Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.
Marc M
MM
Greenberg
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.
Alexander C
AC
Drohat
D044503:5-Methylcytosine / Q000737:chemistry / Q000378:metabolism; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D004260:DNA Repair; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D010084:Oxidation-Reduction; D011485:Protein Binding; D000072417:Protein Domains; D013379:Substrate Specificity; D044502:Thymine DNA Glycosylase / Q000737:chemistry / Q000378:metabolism*
C560974:5-carboxylcytosine; C560973:5-formylcytosine; D009838:Oligodeoxyribonucleotides; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA; D044502:Thymine DNA Glycosylase