Journal of Molecular Modeling

, Volume 16, Issue 7, pp 1213–1222 | Cite as

Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA

  • Juan A. Castelán-Vega
  • Alicia Jiménez-Alberto
  • Rosa M. Ribas-Aparicio
Original Paper

Abstract

M.HgiDII is a methyltransferase (MTase) from Herpetosiphon giganteus that recognizes the sequence GTCGAC. This enzyme belongs to a group of MTases that share a high degree of amino acid similarity, albeit none of them has been thoroughly characterized. To study the catalytic mechanism of M.HgiDII and its interactions with DNA, we performed molecular dynamics simulations with a homology model of M.HgiDII complexed with DNA and S-adenosyl-methionine. Our results indicate that M.HgiDII may not rely only on Glu119 to activate the cytosine ring, which is an early step in the catalysis of cytosine methylation; apparently, Arg160 and Arg162 may also participate in the activation by interacting with cytosine O2. Another residue from the catalytic site, Val118, also played a relevant role in the catalysis of M.HgiDII. Val118 interacted with the target cytosine and kept water molecules from accessing the region of the catalytic pocket where Cys79 interacts with cytosine, thus preventing water-mediated disruption of interactions in the catalytic site. Specific recognition of DNA was mediated mainly by amino acids of the target recognition domain, although some amino acids (loop 80–88) of the catalytic domain may also contribute to DNA recognition. These interactions involved direct contacts between M.HgiDII and DNA, as well as indirect contacts through water bridges. Additionally, analysis of sequence alignments with closely related MTases helped us to identify a motif in the TRD of M.HgiDII that may be relevant to specific DNA recognition.

Keywords

DNA-methyltransferase DNA recognition Homology modeling M.HgiDII Molecular dynamics S-adenosyl-methionine 

References

  1. 1.
    Kozbial PZ, Mushegian AR (2005) Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol 5:19. doi:10.1186/1472-6807-5-19 CrossRefGoogle Scholar
  2. 2.
    Bheemanaik S, Reddy YVR, Rao DN (2006) Structure, function and mechanism of exocyclic DNA methyltransferases. Biochem J 399:177–190CrossRefGoogle Scholar
  3. 3.
    Bujnicki JM (2001) Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. Acta Biochim Pol 48:935–967Google Scholar
  4. 4.
    Tock MR, Dryden DTF (2005) The biology of restriction and anti-restriction. Curr Opin Microbiol 8:466–472CrossRefGoogle Scholar
  5. 5.
    Buryanov Y, Shevchuk T (2005) The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology. Anal Biochem 338:1–11CrossRefGoogle Scholar
  6. 6.
    Klimasauskas S, Weinhold E (2007) A new tool for biotechnology: AdoMet-dependent methyltransferases. Trends Biotechnol 25:99–104CrossRefGoogle Scholar
  7. 7.
    Jeltsch A (2002) Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. ChemBioChem 3:274–293CrossRefGoogle Scholar
  8. 8.
    Malone T, Blumenthal RM, Cheng X (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253:618–632CrossRefGoogle Scholar
  9. 9.
    Estabrook RA, Lipson R, Hopkins B, Reich N (2004) The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes. J Biol Chem 279:31419–31428CrossRefGoogle Scholar
  10. 10.
    Klimasauskas S, Kumar S, Roberts RJ, Cheng X (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76:357–369CrossRefGoogle Scholar
  11. 11.
    Huang N, Banavali NK, MacKerell AD (2003) Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc Natl Acad Sci USA 100:68–73CrossRefGoogle Scholar
  12. 12.
    Estabrook RA, Nguyen TT, Fera N, Reich NO (2009) Coupling Sequence-specific Recognition to DNA Modification. J Biol Chem 284:22690–22696CrossRefGoogle Scholar
  13. 13.
    Zhou H, Purdy MM, Dahlquist FW, Reich NO (2009) The recognition pathway for the DNA cytosine methyltransferase M.HhaI. Biochemistry 48:7807–7816CrossRefGoogle Scholar
  14. 14.
    Estabrook RA, Reich N (2006) Observing an induced-fit mechanism during sequence-specific DNA methylation. J Biol Chem 281:37205–37214CrossRefGoogle Scholar
  15. 15.
    Shieh F, Reich NO (2007) AdoMet-dependent methyl-transfer: Glu119 is essential for DNA C5-cytosine methyltransferase M.HhaI. J Mol Biol 373:1157–1168CrossRefGoogle Scholar
  16. 16.
    Shieh F, Youngblood B, Reich NO (2006) The role of Arg165 towards base flipping, base stabilization and catalysis in M.HhaI. J Mol Biol 362:516–527CrossRefGoogle Scholar
  17. 17.
    Zhang X, Bruice TC (2006) The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/molecular mechanics approach. Proc Natl Acad Sci USA 103:6148–6153CrossRefGoogle Scholar
  18. 18.
    Lau EY, Bruice TC (1999) Active site dynamics of the HhaI methyltransferase: insights from computer simulation. J Mol Biol 293:9–18CrossRefGoogle Scholar
  19. 19.
    Roberts RJ (1994) An amazing distortion in DNA induced by a methyltransferase. Biosci Rep 14:103–117CrossRefGoogle Scholar
  20. 20.
    Szegedi SS, Gumport RI (2000) DNA binding properties in vivo and target recognition domain sequence alignment analyses of wild-type and mutant RsrI [N6-adenine] DNA methyltransferases. Nucleic Acids Res 28:3972–3981CrossRefGoogle Scholar
  21. 21.
    Vilkaitis G, Dong A, Weinhold E, Cheng X, Klimasauskas S (2000) Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J Biol Chem 275:38722–38730Google Scholar
  22. 22.
    Neely RK, Roberts RJ (2008) The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs. BMC Mol Biol 9:48. doi:10.1186/1471-2199-9-48 CrossRefGoogle Scholar
  23. 23.
    Kröger M, Hobom G, Schütte H, Mayer H (1984) Eight new restriction endonucleases from Herpetosiphon giganteus–divergent evolution in a family of enzymes. Nucleic Acids Res 12:3127–3141CrossRefGoogle Scholar
  24. 24.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948CrossRefGoogle Scholar
  25. 25.
    Bryson K, McGuffin LJ, Marsden RL, Ward LL, Sodhi JS, Jones DT (2005) Protein structure prediction servers at University College London. Nucleic Acids Res 33:W36–38CrossRefGoogle Scholar
  26. 26.
    Eswar N, Eramian D, Webb B, Shen M, Sali A (2008) Protein structure modeling with MODELLER. Methods Mol Biol 426:145–159CrossRefGoogle Scholar
  27. 27.
    Melo F, Devos D, Depiereux E, Feytmans E (1997) ANOLEA: a www server to assess protein structures. Proc Int Conf Intell Syst Mol Biol 5:187–190Google Scholar
  28. 28.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefGoogle Scholar
  29. 29.
    Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38CrossRefGoogle Scholar
  30. 30.
    MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616CrossRefGoogle Scholar
  31. 31.
    Mackerell A, Banavali N (2000) All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 21:105–120CrossRefGoogle Scholar
  32. 32.
    Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  33. 33.
    Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–410CrossRefGoogle Scholar
  34. 34.
    Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404CrossRefGoogle Scholar
  35. 35.
    Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802CrossRefGoogle Scholar
  36. 36.
    Bourne PE, Weissig H (2003) Structural bioinformatics. Wiley-Liss, WilmingtonCrossRefGoogle Scholar
  37. 37.
    Koudan EV, Bujnicki JM, Gromova ES (2004) Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy. J Biomol Struct Dyn 22:339–345Google Scholar
  38. 38.
    Bujnicki JM (2000) Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases? Int J Biol Macromol 27:195–204CrossRefGoogle Scholar
  39. 39.
    Reinisch K (1995) The crystal structure of HaeIII methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing. Cell 82:143–153CrossRefGoogle Scholar
  40. 40.
    Darii MV, Cherepanova NA, Subach OM, Kirsanova OV, Raskó T, Slaska-Kiss K, Kiss A, Deville-Bonne D, Reboud-Ravaux M, Gromova ES (2009) Mutational analysis of the CG recognizing DNA methyltransferase SssI: insight into enzyme-DNA interactions. Biochim Biophys Acta. doi:10.1016/j.bbapap. 2009.07.016 Google Scholar
  41. 41.
    Gabbara S, Sheluho D, Bhagwat AS (1995) Cytosine methyltransferase from Escherichia coli in which active site cysteine is replaced with serine is partially active. Biochemistry 34:8914–8923CrossRefGoogle Scholar
  42. 42.
    Kumar S, Horton JR, Jones GD, Walker RT, Roberts RJ, Cheng X (1997) DNA containing 4′-thio-2′-deoxycytidine inhibits methylation by HhaI methyltransferase. Nucleic Acids Res 25:2773–2783CrossRefGoogle Scholar
  43. 43.
    Lauster R, Trautner TA, Noyer-Weidner M (1989) Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains. J Mol Biol 206:305–312CrossRefGoogle Scholar
  44. 44.
    Wintjens R, Liévin J, Rooman M, Buisine E (2000) Contribution of cation-pi interactions to the stability of protein-DNA complexes. J Mol Biol 302:395–410CrossRefGoogle Scholar
  45. 45.
    Reddy CK, Das A, Jayaram B (2001) Do water molecules mediate protein-DNA recognition? J Mol Biol 314:619–632CrossRefGoogle Scholar
  46. 46.
    Rhodes D, Schwabe JW, Chapman L, Fairall L (1996) Towards an understanding of protein-DNA recognition. Philos Trans R Soc Lond B Biol Sci 351:501–509CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Juan A. Castelán-Vega
    • 1
    • 2
  • Alicia Jiménez-Alberto
    • 2
  • Rosa M. Ribas-Aparicio
    • 2
  1. 1.Center for Biologics Evaluation and ResearchUS FDA, CBER/DBPAP [HFM-443]RockvilleUSA
  2. 2.Departamento de MicrobiologíaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalMexicoMexico

Personalised recommendations