Binding of the J-Binding protein to DNA containing glucosylated hmU (Base J) or 5-hmC: Evidence for a rapid conformational change upon DNA binding

Journal of the American Chemical Society

Volumn 134, Issue 32, 2012, Pages 13357-13365

  Heidebrecht, Tatjana ^a   Fish, Alexander ^a   Von Castelmur, Eleonore ^a   Johnson, Kenneth A ^c   Zaccai, Giuseppe ^d   Borst, Piet ^b   Perrakis, Anastassis ^a  

^a Division Biochemistry   (Netherlands)

^b NETHERLANDS CANCER INSTITUTE   (Netherlands)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^d INSTITUT LAUE LANGEVIN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING DOMAIN; CONFORMATIONAL CHANGE; DNA BINDING; EQUILIBRIUM BINDING; FLUORESCENCE POLARIZATION; GLOBAL ANALYSIS; HYDROXYLASES; HYDROXYMETHYLCYTOSINE; KINETIC DATA; LEISHMANIA; NUCLEAR DNA; ONE-STEP REACTIONS; PATHOGENIC PROTOZOA; PRE-STEADY STATE; SECOND-ORDER RATE CONSTANTS; SMALL-ANGLE NEUTRON SCATTERING; SPATIAL PROXIMITY; STOPPED FLOW; TWO-STEP MECHANISMS; TWO-STEP REACTIONS;

BIOCHEMISTRY; HYDROXYLATION; MAMMALS; NEUTRON SCATTERING; OLIGONUCLEOTIDES; RATE CONSTANTS;

DNA;

5 HYDROXYMETHYLCYTOSINE; BETA D GLUCOSYL HYDROXYMETHYLURACIL; OLIGONUCLEOTIDE; OXYGENASE; THYMIDINE; UNCLASSIFIED DRUG; URACIL DERIVATIVE;

ARTICLE; BINDING AFFINITY; BIOSYNTHESIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA BINDING; EQUILIBRIUM CONSTANT; FLUORESCENCE POLARIZATION IMMUNOASSAY; NEUTRON SCATTERING; PROTEIN BINDING;

CARRIER PROTEINS; GLUCOSIDES; KINETICS; MOLECULAR CONFORMATION; PROTEIN BINDING; TIME FACTORS; URACIL;

EID: 84865111457     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja303423t     Document Type: Article

References (41)

1. Cross, M.; Kieft, R.; Sabatini, R.; Wilm, M.; de Kort, M.; van der Marel, G. A.; van Boom, J. H.; van Leeuwen, F.; Borst, P. EMBO J. 1999, 18, 6573
2. Dipaolo, C.; Kieft, R.; Cross, M.; Sabatini, R. Mol. Cell 2005, 17, 441
3. Kieft, R.; Brand, V.; Ekanayake, D. K.; Sweeney, K.; DiPaolo, C.; Reznikoff, W. S.; Sabatini, R. Mol. Biochem. Parasitol. 2007, 156, 24
4. Vainio, S.; Genest, P. A.; ter Riet, B.; van Luenen, H.; Borst, P. Mol. Biochem. Parasitol. 2009, 164, 157
5. Yu, Z.; Genest, P. A.; ter Riet, B.; Sweeney, K.; DiPaolo, C.; Kieft, R.; Christodoulou, E.; Perrakis, A.; Simmons, J. M.; Hausinger, R. P.; van Luenen, H. G.; Rigden, D. J.; Sabatini, R.; Borst, P. Nucleic Acids Res. 2007, 35, 2107
6. Gommers-Ampt, J. H.; Van Leeuwen, F.; De Beer, A. L. J.; Vliegenthart, J. F. G.; Dizdaroglu, M.; Kowalak, J. A.; Crain, P. F.; Borst, P. Cell 1993, 75, 1129
7. Van Leeuwen, F.; Taylor, M. C.; Mondragon, A.; Moreau, H.; Gibson, W.; Kieft, R.; Borst, P. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 2366
8. Toaldo, C. B.; Kieft, R.; Dirks-Mulder, A.; Sabatini, R.; van Luenen, H. G.; Borst, P. Mol. Biochem. Parasitol. 2005, 143, 111
9. Borst, P.; Sabatini, R. Annu. Rev. Microbiol. 2008, 62, 235
10. van Leeuwen, F.; Wijsman, E. R.; Kuyl-Yeheskiely, E.; van der Marel, G. A.; van Boom, J. H.; Borst, P. Nucleic Acids Res. 1996, 24, 2476
11. Van Leeuwen, F.; Kieft, R.; Cross, M.; Borst, P. Mol. Biochem. Parasitol. 2000, 109, 133
12. Cliffe, L. J.; Kieft, R.; Southern, T.; Birkeland, S. R.; Marshall, M.; Sweeney, K.; Sabatini, R. Nucleic Acids Res. 2009, 37, 1452
13. Cliffe, L. J.; Siegel, T. N.; Marshall, M.; Cross, G. A.; Sabatini, R. Nucleic Acids Res. 2010, 38, 3923
14. Ekanayake, D. K.; Minning, T.; Weatherly, B.; Gunasekera, K.; Nilsson, D.; Tarleton, R.; Ochsenreiter, T.; Sabatini, R. Mol. Cell. Biol. 2011, 31, 1690
15. van Luenen, H.; Farris, C.; Jan, S.; Genest, P. A.; Tripathi, P.; Velds, A.; Kerkhoven, R. M.; Nieuwland, M.; Haydock, A.; Ramasamy, G.; Vainio, S.; Heidebrecht, T.; Perrakis, A.; Pagie, L.; van Steensel, B.; Myler, P. J.; Borst, P. Cell 2012, in press.
16. Kriaucionis, S.; Heintz, N. Science 2009, 324, 929
17. Tahiliani, M.; Koh, K. P.; Shen, Y.; Pastor, W. A.; Bandukwala, H.; Brudno, Y.; Agarwal, S.; Iyer, L. M.; Liu, D. R.; Aravind, L.; Rao, A. Science 2009, 324, 930
18. Gu, T. P.; Guo, F.; Yang, H.; Wu, H. P.; Xu, G. F.; Liu, W.; Xie, Z. G.; Shi, L.; He, X.; Jin, S. G.; Iqbal, K.; Shi, Y. G.; Deng, Z.; Szabo, P. E.; Pfeifer, G. P.; Li, J.; Xu, G. L. Nature 2011, 477, 606
19. Guo, J. U.; Su, Y.; Zhong, C.; Ming, G. L.; Song, H. Cell 2011, 145, 423
20. Iqbal, K.; Jin, S. G.; Pfeifer, G. P.; Szabo, P. E. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 3642
21. Ito, S.; D'Alessio, A. C.; Taranova, O. V.; Hong, K.; Sowers, L. C.; Zhang, Y. Nature 2010, 466, 1129
22. Ito, S.; Shen, L.; Dai, Q.; Wu, S. C.; Collins, L. B.; Swenberg, J. A.; He, C.; Zhang, Y. Science 2011, 333, 1300
23. Ko, M.; Bandukwala, H. S.; An, J.; Lamperti, E. D.; Thompson, E. C.; Hastie, R.; Tsangaratou, A.; Rajewsky, K.; Koralov, S. B.; Rao, A. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 14566
24. Ko, M.; Huang, Y.; Jankowska, A. M.; Pape, U. J.; Tahiliani, M.; Bandukwala, H. S.; An, J.; Lamperti, E. D.; Koh, K. P.; Ganetzky, R.; Liu, X. S.; Aravind, L.; Agarwal, S.; Maciejewski, J. P.; Rao, A. Nature 2011, 468, 839
25. Iyer, L. M.; Tahiliani, M.; Rao, A.; Aravind, L. Cell Cycle 2009, 8, 1698
26. Sabatini, R.; Meeuwenoord, N.; van Boom, J. H.; Borst, P. J. Biol. Chem. 2002, 277, 958
27. Sabatini, R.; Meeuwenoord, N.; van Boom, J. H.; Borst, P. J. Biol. Chem. 2002, 277, 28150
28. Grover, R. K.; Pond, S. J.; Cui, Q.; Subramaniam, P.; Case, D. A.; Millar, D. P.; Wentworth, P., Jr. Angew. Chem., Int. Ed. Engl. 2007, 46, 2839
29. Robertson, A. B.; Dahl, J. A.; Ougland, R.; Klungland, A. Nat. Protoc. 2012, 7, 340
30. Robertson, A. B.; Dahl, J. A.; Vagbo, C. B.; Tripathi, P.; Krokan, H. E.; Klungland, A. Nucleic Acids Res. 2011, 39, e55
31. Robertson, J.; Robertson, A. B.; Klungland, A. Biochem. Biophys. Res. Commun. 2011, 411, 40
32. Heidebrecht, T.; Christodoulou, E.; Chalmers, M. J.; Jan, S.; Ter Riet, B.; Grover, R. K.; Joosten, R. P.; Littler, D.; van Luenen, H.; Griffin, P. R.; Wentworth, P., Jr.; Borst, P.; Perrakis, A. Nucleic Acids Res. 2011, 39, 5715
33. Stricher, F.; Martin, L.; Barthe, P.; Pogenberg, V.; Mechulam, A.; Menez, A.; Roumestand, C.; Veas, F.; Royer, C.; Vita, C. Biochem. J. 2005, 390, 29
34. Johnson, K. A.; Simpson, Z. B.; Blom, T. Anal. Biochem. 2009, 387, 20
35. Johnson, K. A. Methods Enzymol. 2009, 467, 601
36. Serdyuk, I. N.; Zaccai, N.; Zaccai, G. Methods in Molecular Biophysics: Structure, Dynamics, Function; Cambridge University Press, Cambridge, UK: 2007.
37. Johnson, K. A.; Simpson, Z. B.; Blom, T. Anal. Biochem. 2009, 387, 30
38. Jacrot, B. Rep. Prog. Phys. 1976, 39, 911
39. Stuhrmann, H. B. Acta Crystallogr., Sect. A 2008, 64, 181
40. Dessen, P.; Blanquet, S.; Zaccai, G.; Jacrot, B. J. Mol. Biol. 1978, 126, 293
41. Bonneté, F.; Ebel, C.; Zaccai, G.; Eisenberg, H. J. Chem. Soc., Faraday Trans. 1993, 89, 2659