Biochemistry and Molecular Biology
108 N. Greene St., 419
Education and Training
University of Maryland, BS, Aerospace Engineering
University of Maryland School of Medicine, PhD, Biochemistry and Molecular Biology
Johns Hopkins University School of Medicine, NIST and Center for Advanced Research in Biotechnology, Postdoctoral Fellow
Our research centers on two broad areas, DNA repair and epigenetic regulation. The nucleobases of DNA are amenable to a broad range of chemical alterations, a feature that enables enzyme-mediated modifications but also allows for threatening DNA damage. We study enzymes that find and repair DNA lesions, thereby maintaining genomic integrity and protecting against cancer and other diseases. We also investigate enzymes that perform essential functions in epigenetic regulation, by acting on modified DNA bases. We use a broad range of biochemical, biophysical, structural, and molecular approaches, and collaborate with many other research groups. Some of our current research interests are summarized below.
DNA Repair, Epigenetics and DNA methylation, Enzymology, NMR, Structural Biology, SUMO modification
Excision of 5-carboxylcytosine by Thymine DNA Glycosylase, J Am Chem Soc ePub 6 Nov 2019, doi: 10.1021/jacs.9b10376
Dow BJ, Malik SS, Drohat AC (2019) Defining the Role of Nucleotide Flipping in Enzyme Specificity Using 19F NMR, J Am Chem Soc 141, 4952-62.
Coey CT, Drohat AC (2018) Defining the impact of sumoylation on substrate binding and catalysis by thymine DNA glycosylase, Nucleic Acids Res 46, 5159-70.
Pidugu LS, Flowers JW, Coey CT, Pozharski E, Greenberg MM, Drohat AC (2016) Structural basis for excision of 5-formylcytosine by Thymine DNA glycosylase, Biochemistry 55, 6205-8.
Drohat AC and Coey CT (2016) Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA, Chem Rev 116, 12711-29.
Coey CT, Fitzgerald ME, Maiti A, Reiter KH, Guzzo CM, Matunis MJ, Drohat AC (2014) E2-mediated small ubiquitin-like modifier (SUMO) modification of thymine DNA glycosylase is efficient but not selective for the enzyme-product complex, J Biol Chem 289, 15810-9.
Maiti A, Michelson AZ, Armwood CJ, Lee JK, Drohat AC (2013) Divergent Mechanisms for Enzymatic Excision of 5-formylcytosine and 5-carboxylcytosine from DNA, J Am Chem Soc 135, 15813-22.
Maiti A, Noon MS, MacKerell AD Jr, Pozhaski E, Drohat AC (2012) Lesion Processing by a Repair Enzyme is Severely Curtailed by Residues Needed to Prevent Aberrant Activity on Undamaged DNA, Proc Natl Acad Sci USA 109, 891-6.
Maiti A, Drohat AC (2011) Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: Potential implications for active demethylation of CpG sites, J Biol Chem 286, 35334-8.
DNA Repair – Avoiding mutations caused by mC deamination
Often termed the “5th base” in DNA, 5-methylcytosine (mC) is a key epigenetic mark in eukaryotes, and it functions in restriction modification systems of archaea and bacteria. However, mC also threatens genetic and epigenetic integrity. Deamination of mC to T generates G/T mispairs, and, upon replication, CàT transitions. Through this process, mC deamination causes many point mutations in cancer and genetic disease. Two human glycosylases remove T from G/T mispairs, TDG (thymine DNA glycosylase) and MBD4 (methyl binding domain IV). Like other glycosylases, they flip a damaged base into their active site and cleave the base-sugar bond; follow-on base excision repair (BER) enzymes complete the repair process. While most glycosylases excise bases that are foreign to DNA (e.g., uracil), these mismatch enzymes remove a canonical base, thymine, from rare G/T mispairs but not from the vast background of A:T pairs. Because aberrant action on A:T pairs can be mutagenic and cytotoxic, specificity is critical for these enzymes, and we are studying how it is attained. We also study how TDG and MBD4 recognize other damaged bases, including uracil and 5-fluorouracil (5FU), among others. TDG excision of 5FU contributes to the antitumor effects of 5FU, which is used to treat cancer.
Epigenetic Regulation - Base Excision Repair in active DNA Demethylation
Methyltransferases are known to convert C to mC, but the process for reversing this epigenetic modification had remained unclear. One mechanism involves DNA replication without subsequent remethylation. Recent studies establish a pathway for active DNA demethylation, involving TET (ten-eleven translocation) enzymes and TDG-initiated BER (Fig. 1). TET enzymes catalyze stepwise oxidation of mC, to give 5-hydroxymethyl-C (hmC), then 5-formyl-C (fC), and 5-carboxyl-C (caC). TDG excises fC and caC, and subsequent BER steps restore cytosine. This central function in epigenetic regulation likely explains findings that TDG is essential for embryonic development. We study the role of TDG and other BER enzymes in active DNA demethylation.
Protein Regulation by SUMO binding and SUMO conjugation
TDG can be covalently modified by SUMO (small ubiquitin-like modifier) proteins, and it also features a SUMO interacting motif (SIM) that binds non-covalentlyto SUMO domains. The SIM can bind free SUMO, a SUMO domain that is tethered to another protein, and intramolecularSUMO (tethered to TDG). We are investigating the effect of SUMO binding and SUMO conjugation on TDG function(s), and testing the current paradigm that SUMO modification of product-bound TDG is needed to relieve product inhibition and allow for efficient catalytic turnover. We are also studying how SUMO modification of TDG is regulated in cells.
Nov 2019: We recently solved the first high-resolution structures of TDG bound to DNA with cadC (5-carboxyl-dC) in its active site. The structures unveil detailed enzyme-substrate interactions that mediate recognition and removal of caC, many involving water molecules and they redefine the structural context for TDG excision of caC. Three new structures were submitted to the PDB and will now be released with online publicaiton of a paper describing the new structures in J Am Chem Soc (https://pubs.acs.org/doi/10.1021/jacs.9b10376).
Aug 2019: We were thrilled to be awarded an Administrative Supplement from the NIH to procure a new 19F-capable cryoprobe for our 600 NMR MHz spectrometer (3R01GM072711-14S1). 19F NMR is a powerfull approach for studying structure and dynamics in biological systems, as exemplified in our 2019 JACS paper. The new probe offers a massive 7-fold increase in 19F sensitivity compared to our current probe and will dramatically expand our research capabilites using 19F NMR.