5JXY: Enzyme-substrate Complex Of Tdg Catalytic Domain Bound To A G/u Analog

Citation:
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 TDG82-308, a new construct containing 29 more N-terminal residues than TDG111-308, 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 TDG82-308 Nevertheless, G.T substrate affinity and glycosylase activity of TDG82-308 greatly exceeds that of TDG111-308 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 TDG82-308 (1.54 A) and TDG111-308 (1.71 A), revealing new enzyme-substrate contacts, direct and water-mediated. We also report a structure of the TDG82-308 product complex (1.70 A). TDG82-308 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.
PDB ID: 5JXYDownload
MMDB ID: 143560
PDB Deposition Date: 2016/5/13
Updated in MMDB: 2016/12
Experimental Method:
x-ray diffraction
Resolution: 1.71  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 5JXY: trimeric; determined by author and by software (PISA)
Molecular Components in 5JXY
Label Count Molecule
Protein (1 molecule)
1
G/T Mismatch-specific Thymine DNA Glycosylase(Gene symbol: TDG)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (28-mer)
Molecule annotation
1
DNA (28-mer)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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