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Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

Liu, Monica Yun, Torabifard, Hedieh, Crawford, Daniel J, DeNizio, Jamie E, Cao, Xing-Jun, Garcia, Benjamin A, Cisneros, G Andrés, Kohli, Rahul M·2017·Nature Chemical Biology
DOI 10.1038/nchembio.2250PMC PMC5370579
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  1. Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009). · DOI · Paper page
  2. Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133 (2010). · DOI · Paper page
  3. Pfaffeneder, T. et al. The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew. Chem. Int. Edn Engl. 50, 7008–7012 (2011). · DOI
  4. He, Y.F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303–1307 (2011). · DOI
  5. Bachman, M. et al. 5-Hydroxymethylcytosine is a predominantly stable DNA modification. Nat. Chem. 6, 1049–1055 (2014). · DOI
  6. Bachman, M. et al. 5-Formylcytosine can be a stable DNA modification in mammals. Nat. Chem. Biol. 11, 555–557 (2015). · DOI
  7. Wu, H. & Zhang, Y. Charting oxidized methylcytosines at base resolution. Nat. Struct. Mol. Biol. 22, 656–661 (2015). · DOI
  8. Liu, M.Y., DeNizio, J.E., Schutsky, E.K. & Kohli, R.M. The expanding scope and impact of epigenetic cytosine modifications. Curr. Opin. Chem. Biol. 33, 67–73 (2016). · DOI
  9. Zheng, G., Fu, Y. & He, C. Nucleic acid oxidation in DNA damage repair and epigenetics. Chem. Rev. 114, 4602–4620 (2014). · DOI
  10. Hu, L. et al. Structural insight into substrate preference for TET-mediated oxidation. Nature 527, 118–122 (2015). · DOI
  11. Hu, L. et al. Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. Cell 155, 1545–1555 (2013). · DOI
  12. Lu, J. et al. A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2). Phys. Chem. Chem. Phys. 18, 4728–4738 (2016). · DOI
  13. Maiti, A. & Drohat, A.C. Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J. Biol. Chem. 286, 35334–35338 (2011). · DOI
  14. Weber, A.R. et al. Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanism. Nat. Commun. 7, 10806 (2016). · DOI
  15. Iurlaro, M. et al. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biol. 14, R119 (2013). · DOI
  16. Crawford, D.J. et al. Tet2 catalyzes stepwise 5-methylcytosine oxidation by an iterative and de novo mechanism. J. Am. Chem. Soc. 138, 730–733 (2016). · DOI
  17. Fang, D., Lord, R.L. & Cisneros, G.A. Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB. J. Phys. Chem. B 117, 6410–6420 (2013). · DOI
  18. Fang, D. & Cisneros, G.A. Alternative pathway for the reaction catalyzed by DNA dealkylase AlkB from ab initio QM/MM calculations. J. Chem. Theory Comput. 10, 5136–5148 (2014). · DOI
  19. Hashimoto, H. et al. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA. Nucleic Acids Res. 43, 10713–10721 (2015). · DOI
  20. Abdel-Wahab, O. et al. Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood 114, 144–147 (2009). · DOI · Paper page
  21. Scourzic, L., Mouly, E. & Bernard, O.A. TET proteins and the control of cytosine demethylation in cancer. Genome Med. 7, 9 (2015). · DOI
  22. Cliffe, L.J. et al. JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Res. 37, 1452–1462 (2009). · DOI
  23. Bullard, W., Lopes da Rosa-Spiegler, J., Liu, S., Wang, Y. & Sabatini, R. Identification of the glucosyltransferase that converts hydroxymethyluracil to base J in the trypanosomatid genome. J. Biol. Chem. 289, 20273–20282 (2014). · DOI
  24. Pei, J., Kim, B.H. & Grishin, N.V. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res. 36, 2295–2300 (2008). · DOI
  25. Hu, X. et al. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 14, 512–522 (2014). · DOI
  26. Neri, F. et al. TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway. Oncogene 34, 4168–4176 (2015). · DOI
  27. Gu, T.P. et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477, 606–610 (2011). · DOI
  28. Liu, M.Y., DeNizio, J.E. & Kohli, R.M. Quantification of oxidized 5-methylcytosine bases and TET enzyme activity. Methods Enzymol. 573, 365–385 (2016). · DOI
  29. Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010). · DOI · Paper page
  30. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. & Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926 (1983). · DOI
  31. Dolinsky, T.J., Nielsen, J.E., McCammon, J.A. & Baker, N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32, W665–W667 (2004). · DOI
  32. Dolinsky, T.J. et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35, W522–W525 (2007). · DOI
  33. Olsson, M.H., Søndergaard, C.R., Rostkowski, M. & Jensen, J.H. PROPKA3: Consistent treatment of internal and surface residues in empirical pKa predictions. J. Chem. Theory Comput. 7, 525–537 (2011). · DOI
  34. Bradbrook, G.M. et al. X-Ray and molecular dynamics studies of concanavalin-A glucoside and mannoside complexes relating structure to thermodynamics of binding. J. Chem. Soc., Faraday Trans. 94, 1603–1611 (1998). · DOI
  35. Oda, A., Yamaotsu, N. & Hirono, S. New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models. J. Comput. Chem. 26, 818–826 (2005). · DOI
  36. Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995). · DOI
  37. Roe, D.R. & Cheatham, T.E. III. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 9, 3084–3095 (2013). · DOI
  38. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38, 27–28 (1996). · DOI · Paper page
  39. Johnson, E.R. et al. Revealing noncovalent interactions. J. Am. Chem. Soc. 132, 6498–6506 (2010). · DOI
  40. Contreras-García, J. et al. NCIPLOT: a program for plotting non-covalent interaction regions. J. Chem. Theory Comput. 7, 625–632 (2011). · DOI
  41. Graham, S.E., Syeda, F. & Cisneros, G.A. Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I. Biochemistry 51, 2569–2578 (2012). · DOI
  42. Elias, A.A. & Cisneros, G.A. Computational study of putative residues involved in DNA synthesis fidelity checking in Thermus aquaticus DNA polymerase I. Adv. Protein Chem. Struct. Biol. 96, 39–75 (2014). · DOI
  43. Dewage, S.W. & Cisneros, G.A. Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB). J. Phys. Chem. B 119, 3669–3677 (2015). · DOI
  44. Cui, Q. & Karplus, M. Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase. Adv. Protein Chem. 66, 315–372 (2003). · DOI
  45. Martí, S. et al. Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case. Chemistry 9, 984–991 (2003). · DOI
  46. Senn, H.M., O'Hagan, D. & Thiel, W. Insight into enzymatic C-F bond formation from QM and QM/MM calculations. J. Am. Chem. Soc. 127, 13643–13655 (2005). · DOI
  47. Cisneros, G.A. et al. Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J. Am. Chem. Soc. 131, 1550–1556 (2009). · DOI
  48. Maiti, A., Michelson, A.Z., Armwood, C.J., Lee, J.K. & Drohat, A.C. Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA. J. Am. Chem. Soc. 135, 15813–15822 (2013). · DOI
  49. Morgan, M.T., Bennett, M.T. & Drohat, A.C. Excision of 5-halogenated uracils by human thymine DNA glycosylase. Robust activity for DNA contexts other than CpG. J. Biol. Chem. 282, 27578–27586 (2007). · DOI

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Metadata

Authors
Liu, M. Y., Torabifard, H., Crawford, D. J., DeNizio, J. E., Cao, X.-J., Garcia, B. A., Cisneros, G. A., & Kohli, R. M.
Venue
Nature Chemical Biology
Publisher
Springer Science and Business Media LLC
Published
2016-12-05
Volume
13
Issue
2
Pages
181-187
ISSN
  • 1552-4450
  • 1552-4469
DOI
10.1038/nchembio.2250
PMC
PMC5370579
Cited by
78
References
6
Language
en
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CoChat. (2026). Citation check: Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. https://app.cochat.ai/papers/10.1038/nchembio.2250
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Liu, M. Y., Torabifard, H., Crawford, D. J., DeNizio, J. E., Cao, X.-J., Garcia, B. A., Cisneros, G. A., & Kohli, R. M. (2017). Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nature Chemical Biology. https://doi.org/10.1038/nchembio.2250