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Crystal structure of human methyl-binding domain IV glycosylase bound to abasic DNA.

Manvilla BA, Maiti A, Begley MC, Toth EA, Drohat AC
J Mol Biol 420 164-75 (2012)
Cited: 27 times
EuropePMC logo PMID: 22560993

Abstract

The mammalian repair protein MBD4 (methyl-CpG-binding domain IV) excises thymine from mutagenic G·T mispairs generated by deamination of 5-methylcytosine (mC), and downstream base excision repair proteins restore a G·C pair. MBD4 is also implicated in active DNA demethylation by initiating base excision repair of G·T mispairs generated by a deaminase enzyme. The question of how mismatch glycosylases attain specificity for excising thymine from G·T, but not A·T, pairs remains largely unresolved. Here, we report a crystal structure of the glycosylase domain of human MBD4 (residues 427-580) bound to DNA containing an abasic nucleotide paired with guanine, providing a glimpse of the enzyme-product complex. The mismatched guanine remains intrahelical, nestled into a recognition pocket. MBD4 provides selective interactions with the mismatched guanine (N1H, N2H(2)) that are not compatible with adenine, which likely confer mismatch specificity. The structure reveals no interactions that would be expected to provide the MBD4 glycosylase domain with specificity for acting at CpG sites. Accordingly, we find modest 1.5- to 2.7-fold reductions in G·T activity upon altering the CpG context. In contrast, 37- to 580-fold effects were observed previously for thymine DNA glycosylase. These findings suggest that specificity of MBD4 for acting at CpG sites depends largely on its methyl-CpG-binding domain, which binds preferably to G·T mispairs in a methylated CpG site. MBD4 glycosylase cannot excise 5-formylcytosine (fC) or 5-carboxylcytosine (caC), intermediates in a Tet (ten eleven translocation)-initiated DNA demethylation pathway. Our structure suggests that MBD4 does not provide the electrostatic interactions needed to excise these oxidized forms of mC.

Reviews - 4dk9 mentioned but not cited (1)

  1. Recent advances in the structural mechanisms of DNA glycosylases. Brooks SC, Adhikary S, Rubinson EH, Eichman BF. Biochim Biophys Acta 1834 247-271 (2013)

Articles - 4dk9 mentioned but not cited (5)

  1. Crystal structure of human methyl-binding domain IV glycosylase bound to abasic DNA. Manvilla BA, Maiti A, Begley MC, Toth EA, Drohat AC. J Mol Biol 420 164-175 (2012)
  2. Search for Modified DNA Sites with the Human Methyl-CpG-Binding Enzyme MBD4. Yakovlev DA, Kuznetsova AA, Fedorova OS, Kuznetsov NA. Acta Naturae 9 88-98 (2017)
  3. Structural Insights into the Mechanism of Base Excision by MBD4. Pidugu LS, Bright H, Lin WJ, Majumdar C, Van Ostrand RP, David SS, Pozharski E, Drohat AC. J Mol Biol 433 167097 (2021)
  4. Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4. Ouzon-Shubeita H, Jung H, Lee MH, Koag MC, Lee S. Biochem J 477 1601-1612 (2020)
  5. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)


Reviews citing this publication (6)

  1. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites. Bellacosa A, Drohat AC. DNA Repair (Amst) 32 33-42 (2015)
  2. Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA. Drohat AC, Coey CT. Chem Rev 116 12711-12729 (2016)
  3. Readers of DNA methylation, the MBD family as potential therapeutic targets. Ginder GD, Williams DC. Pharmacol Ther 184 98-111 (2018)
  4. On the potential role of active DNA demethylation in establishing epigenetic states associated with neural plasticity and memory. Li X, Wei W, Ratnu VS, Bredy TW. Neurobiol Learn Mem 105 125-132 (2013)
  5. Single nucleotide polymorphisms in DNA glycosylases: From function to disease. D'Errico M, Parlanti E, Pascucci B, Fortini P, Baccarini S, Simonelli V, Dogliotti E. Free Radic Biol Med 107 278-291 (2017)
  6. Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets. Hans F, Senarisoy M, Bhaskar Naidu C, Timmins J. Int J Mol Sci 21 E9226 (2020)

Articles citing this publication (15)

  1. Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Hashimoto H, Zhang X, Cheng X. Nucleic Acids Res 40 8276-8284 (2012)
  2. Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA. Moréra S, Grin I, Vigouroux A, Couvé S, Henriot V, Saparbaev M, Ishchenko AA. Nucleic Acids Res 40 9917-9926 (2012)
  3. Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4. Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M. J Biol Chem 288 6351-6362 (2013)
  4. Structural characterization of a mouse ortholog of human NEIL3 with a marked preference for single-stranded DNA. Liu M, Imamura K, Averill AM, Wallace SS, Doublié S. Structure 21 247-256 (2013)
  5. Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues. Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC. Nucleic Acids Res 44 10248-10258 (2016)
  6. Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches. Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN, Williams DC. Nucleic Acids Res 42 11218-11232 (2014)
  7. Pre-steady-state fluorescence analysis of damaged DNA transfer from human DNA glycosylases to AP endonuclease APE1. Kuznetsova AA, Kuznetsov NA, Ishchenko AA, Saparbaev MK, Fedorova OS. Biochim Biophys Acta 1840 3042-3051 (2014)
  8. Defining the Role of Nucleotide Flipping in Enzyme Specificity Using 19F NMR. Dow BJ, Malik SS, Drohat AC. J Am Chem Soc 141 4952-4962 (2019)
  9. 5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. Brooks SC, Fischer RL, Huh JH, Eichman BF. Biochemistry 53 2525-2532 (2014)
  10. Defining the impact of sumoylation on substrate binding and catalysis by thymine DNA glycosylase. Coey CT, Drohat AC. Nucleic Acids Res 46 5159-5170 (2018)
  11. Molecular characterization of a putative plant homolog of MBD4 DNA glycosylase. Ramiro-Merina Á, Ariza RR, Roldán-Arjona T. DNA Repair (Amst) 12 890-898 (2013)
  12. Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans. Sarre A, Ökvist M, Klar T, Hall DR, Smalås AO, McSweeney S, Timmins J, Moe E. J Struct Biol 191 87-99 (2015)
  13. Transcriptional repressor domain of MBD1 is intrinsically disordered and interacts with its binding partners in a selective manner. Hameed UF, Lim J, Zhang Q, Wasik MA, Yang D, Swaminathan K. Sci Rep 4 4896 (2014)
  14. Divergent structures of Mammalian and gammaherpesvirus uracil DNA glycosylases confer distinct DNA binding and substrate activity. Mu Y, Zelazowska MA, Chen Z, Plummer JB, Dong Q, Krug LT, McBride KM. DNA Repair (Amst) 128 103515 (2023)
  15. Backbone Conformational Equilibrium in Mismatched DNA Correlates with Enzyme Activity. Westwood MN, Pilarski A, Johnson C, Mamoud S, Meints GA. Biochemistry 62 2816-2827 (2023)


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