5JXY

Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog

Summary for 5JXY

• Entry DOI: 10.2210/pdb5jxy/pdb
• Related: 3UFJ 5HF7
• Descriptor: G/T mismatch-specific thymine DNA glycosylase, DNA (28-MER), ... (4 entities in total)
• Functional Keywords: protein-dna complex, hydrolase-dna complex, hydrolase/dna
• Biological source: Homo sapiens (Human); More
• Cellular location: Nucleus : Q13569
• Total number of polymer chains: 3
• Total formula weight: 40302.73

Authors

Pidugu, L.S.,Pozharski, E.,Malik, S.S.,Drohat, A.C. (deposition date: 2016-05-13, release date: 2016-09-28, Last modification date: 2023-09-27)

Primary citation

Coey, C.T.,Malik, S.S.,Pidugu, L.S.,Varney, K.M.,Pozharski, E.,Drohat, A.C.
Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues.
Nucleic Acids Res., 44:10248-10258, 2016

PubMed Abstract: Thymine DNA Glycosylase (TDG) is a base excision repair enzyme functioning in DNA repair and epigenetic regulation. TDG removes thymine from mutagenic G·T mispairs arising from deamination of 5-methylcytosine (mC), and it processes other deamination-derived lesions including uracil (U). Essential for DNA demethylation, TDG excises 5-formylcytosine and 5-carboxylcytosine, derivatives of mC generated by Tet (ten-eleven translocation) enzymes. Here, we report structural and functional studies of TDG, a new construct containing 29 more N-terminal residues than TDG, the construct used for previous structures of DNA-bound TDG. Crystal structures and NMR experiments demonstrate that most of these N-terminal residues are disordered, for substrate- or product-bound TDG Nevertheless, G·T substrate affinity and glycosylase activity of TDG greatly exceeds that of TDG and is equivalent to full-length TDG. We report the first high-resolution structures of TDG in an enzyme-substrate complex, for G·U bound to TDG (1.54 Å) and TDG (1.71 Å), revealing new enzyme-substrate contacts, direct and water-mediated. We also report a structure of the TDG product complex (1.70 Å). TDG forms unique enzyme-DNA interactions, supporting its value for structure-function studies. The results advance understanding of how TDG recognizes and removes modified bases from DNA, particularly those resulting from deamination.

PubMed: 27580719
DOI: 10.1093/nar/gkw768

Experimental method

X-RAY DIFFRACTION (1.71 Å)