Background: Thymine DNA glycosylase is essential for active DNA demethylation and embryonic development. Results: TDG rapidly excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), products of Tet-mediated oxidation of 5-methylcytosine. Conclusion: Excision of fC and caC is consistent with TDG specificity for removing modified C or mC from CpG sites. Significance: The results suggest that active DNA demethylation could involve TDG excision of Tet-produced fC (or caC) and subsequent BER.

Initiating the DNA base excision repair pathway, DNA glycosylases find and hydrolytically excise damaged bases from DNA. While some DNA glycosylases exhibit narrow specificity, others remove multiple forms of damage. Human thymine DNA glycosylase (hTDG) cleaves thymine from mutagenic G·T mispairs and recognizes many additional lesions, and has a strong preference for nucleobases paired with guanine rather than adenine. Yet, hTDG avoids cytosine, despite the millionfold excess of normal G·C pairs over G·T mispairs. The mechanism of this remarkable and essential specificity has remained obscure. Here, we examine the possibility that hTDG specificity depends on the stability of the scissile base-sugar bond by determining the maximal activity (k max ) against a series of nucleobases with varying leaving group ability. We find that hTDG removes 5-fluorouracil 78-fold faster than uracil and 5-chlorouracil 572-fold faster than thymine, differences that can be attributed predominantly to leaving group ability. Moreover, hTDG readily excises cytosine analogues with improved leaving ability, including 5-fluorocytosine, 5-bromocytosine, and 5-hydroxycytosine, indicating that cytosine has access to the active site. A plot of log(k max ) versus leaving group pK a reveals a Brønsted-type linear free energy relationship with a large negative slope of β lg = −1.6 ± 0.2, consistent with a highly dissociative reaction mechanism. Further, we find that the hydrophobic active site of hTDG contributes to its specificity by enhancing the inherent differences in substrate reactivity. Thus, hTDG specificity depends on N-glycosidic bond stability, and the discrimination against cytosine is due largely to its very poor leaving ability rather than its exclusion from the active site.

5-methylcytosine (mC) is an epigenetic mark that impacts transcription, development, and genome stability, and aberrant DNA methylation contributes to aging and cancer. Active DNA demethylation involves stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), and potentially 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and restoration of cytosine via follow-on base excision repair. Here, we investigate the mechanism for TDG excision of fC and caC. We find that 5-carboxyl-2′-deoxycytidine ionizes with pKa values of 4.28 (N3) and 2.45 (carboxyl), confirming that caC exists as a monoanion at physiological pH. Calculations do not support the proposal that G·fC and G·caC base pairs adopt a wobble structure that is recognized by TDG. Previous studies show that N-glycosidic bond hydrolysis follows a stepwise (SN1) mechanism, and that TDG activity increases with pyrimidine N1 acidity, i.e., leaving-group quality of the target base. Calculations here show that fC and the neutral tautomers of caC are acidic relative to other TDG substrates, but the caC monoanion exhibits poor acidity and likely resists TDG excision. While fC activity is independent of pH, caC excision is acid catalyzed, and the pH profile indicates that caC ionizes in the enzyme-substrate complex with an apparent pKa of 5.8, likely at N3. Mutational analysis reveals that Asn191 is essential for excision of caC but dispensable for fC activity, indicating that N191 may stabilize N3-protonated forms of caC to facilitate acid catalysis, and suggesting that N191A-TDG could potentially be useful for studying DNA demethylation in cells.

Cytosine methylation at CpG dinucleotides produces m 5 CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m 5 C deamination yields mutagenic G⅐T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G⅐T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G⅐C pair. hTDG is inactive against normal A⅐T pairs, and is most effective for G⅐T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG cat ) in complex with abasic DNA, at 2.8 Å resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG cat can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted in vivo, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity.CpG site ͉ DNA repair ͉ G⅐T mismatch ͉ deamination ͉ 5-methylcytosine H uman thymine DNA glycosylase (hTDG) belongs to the uracil DNA glycosylase (UDG) superfamily of enzymes that share a common ␣/␤ fold and promote genomic integrity by removing mutagenic uracil bases from DNA (1, 2). Initiating the base excision repair pathway, these enzymes use a remarkable nucleotide-flipping mechanism to extrude damaged nucleobases from the DNA helix and cleave the base-sugar (N-glycosidic) bond, producing an abasic (or AP) site in the DNA (3). Together, hTDG and the Escherichia coli mismatch-specific uracil DNA glycosylase (eMUG) are the most thoroughly characterized members of the TDG/MUG family (4-6). These enzymes excise a variety of damaged bases (X), and typically exhibit a strong preference for lesions in G⅐X versus A⅐X pairs (7-12). Like its eukaryotic orthologs, hTDG (410 residues) contains a conserved catalytic core (residues 121-300) flanked by more divergent Nand C-terminal domains (6); the former enhances DNA binding and G⅐T repair activity to some extent (13,14), and the latter contains a site for SUMO conjugation (K330), a modification that decreases the DNA-binding affinity of hTDG (15,16).A recent structure of the hTDG catalytic domain (residues 117-332, conjugated to SUMO-1) reveals strong similarity to the structure of...

Summary During eukaryotic DNA interstrand cross-link (ICL) repair, cross-links are resolved (“unhooked”) by nucleolytic incisions surrounding the lesion. In vertebrates, ICL repair is triggered when replication forks collide with the lesion, leading to FANCI-FANCD2-dependent unhooking and formation of a double-strand break (DSB) intermediate. Using Xenopus egg extracts, we describe here a replication-coupled ICL repair pathway that does not require incisions or FANCI-FANCD2. Instead, the ICL is unhooked when one of the two N-glycosyl bonds forming the cross-link is cleaved by the DNA glycosylase NEIL3. Cleavage by NEIL3 is the primary unhooking mechanism for psoralen- and abasic site-ICLs. When N-glycosyl bond cleavage is prevented, unhooking occurs via FANCI-FANCD2-dependent incisions. In summary, we identify an incision-independent unhooking mechanism that avoids DSB formation and represents the preferred pathway of ICL repair in a vertebrate cell-free system.

The three-dimensional structure of Ca2+-bound rat S100B(betabeta) has been determined using data from a series of two-dimensional (2D), three-dimensional (3D), and four-dimensional (4D) nuclear magnetic resonance (NMR) experiments. Each S100beta subunit (91 residues) contains four helixes (helix 1, E2-R20; helix 2, K29-N38; helix 3, Q50-D61; and helix 4, F70-A83) and one antiparallel beta-sheet (strand 1, K26-K28; and strand 2, E67-D69) which brings the normal and pseudo EF-hands together. As found previously for rat apo-S100B(betabeta) [Drohat, A. C., et al. (1996) Biochemistry 35, 11577-11588], helixes 1, 1', 4, and 4' associate to form an X-type four-helix bundle at the symmetric dimer interface. Additionally, Ca2+ binding does not significantly change the interhelical angle of helixes 1 and 2 in the pseudo EF-hand (apo, Omega1-2 = 132 +/- 4 degrees; and Ca2+-bound, Omega1-2 = 137 +/- 5 degrees). However, the interhelical angle of helixes 3 and 4 in the normal EF-hand (Omega3-4 = 106 +/- 4 degrees) changed significantly upon the addition of Ca2+ (DeltaOmega3-4 = 112 +/- 5 degrees) and is similar to that of the Ca2+-bound EF-hands in calbindin D9K, calmodulin, and troponin (84 degrees

S100B(beta beta), a member of the S100 protein family, is a Ca(2+)-binding protein with noncovalent interactions at its dimer interface. Each apo-S100 beta subunit (91 residues) has four alpha-helices and a small antiparallel beta-sheet, consistent with two predicted helix-loop-helix Ca(2+)-binding domains known as EF-hands [Amburgey et al. (1995) J. Biomol. NMR 6, 171-179]. The three-dimensional solution structure of apo-S100B(beta beta) from rat has been determined using 2672 distance (14.7 per residue) and 88 dihedral angle restraints derived from multidimensional nuclear magnetic resonance spectroscopy. Apo-S100B (beta beta) is found to be globular and compact with an extensive hydrophobic core and a highly charged surface, consistent with its high solubility. At the symmetric dimer interface, 172 intermolecular nuclear Overhauser effect correlations (NOEs) define the antiparallel alignment of helix I with I' and of helix IV with IV'. The perpendicular association of these pairs of antiparallel helices forms an X-type four-helical bundle at the dimer interface. Whereas, the four helices within each apo-S100 beta subunit adopt a unicornate-type four-helix bundle, with helix I protruding from the parallel bundle of helices II, III, and IV. Accordingly, the orientation of helix III relative to helices I, II, and IV in each subunit differs significantly from that known for other Ca(2+)-binding proteins. Indeed, the interhelical angle (omega) observed in the C-terminal EF-hand of apo-S100 beta is -142 degrees, whereas omega ranges from 118 degrees to 145 degrees in the apo state and from 84 degrees to 128 degrees in the Ca(2+)-bound state for the EF-hands of calbindin D9k, calcyclin, and calmodulin. Thus, a significant conformational change in the C-terminal EF-hand would be required for it to adopt a structure typical of the Ca(2+)-bound state, which could readily explain the dramatic spectral effects observed upon the addition of Ca2+ to apo-S100B(beta beta).

S100B(beta beta) was found to interact with the tumor suppressor protein, p53, and inhibit its PKC-dependent phosphorylation and tetramer formation [Baudier, J., Delphin, C., Grunwald, D., Khochbin, S., and Lawrence, J. J. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 11627-11631]. Since PKC-dependent phosphorylation at the C-terminus of p53 is known to effect transcription and p53 tetramer formation [Sakaguchi, K., Sakamoto, H., Lewis, M. S., Anderson, C. W., Erickson, J. W., Appella, E., and Xie, D. (1997) Biochemistry 36, 10117-10124], we examined the interaction of S100B(beta beta) with a peptide derived from the C-terminal regulatory domain of p53 (residues 367-388). In this paper, we report that S100B(beta beta) binds to the p53 peptide (CaK3 < or = 23.5 +/- 6.6 microM) in a Ca(2+)-dependent manner, and that the presence of the p53 peptide was found to increase the binding affinity of Ca2+ to S100B(beta beta) by 3-fold using EPR and PRR methods, whereas the peptide had no effect on Zn2+ binding to S100B(beta beta). Fluorescence and NMR spectroscopy experiments show that the p53 peptide binds to a region of S100B(beta beta) that probably includes residues in the "hinge" (S41, L44, E45, E46, I47), C-terminal loop (A83, C84, H85, E86, F87, F88), and helix 3 (V52, V53, V56, T59). Together these data support the notion that S100B(beta beta) inhibits PKC-dependent phosphorylation by binding directly to the C-terminus of p53.