Active site dynamics of the HhaI methyltransferase: insights from computer simulation - PubMed (original) (raw)
. 1999 Oct 15;293(1):9-18.
doi: 10.1006/jmbi.1999.3120.
Affiliations
- PMID: 10512711
- DOI: 10.1006/jmbi.1999.3120
Active site dynamics of the HhaI methyltransferase: insights from computer simulation
E Y Lau et al. J Mol Biol. 1999.
Abstract
A molecular dynamics study was performed on the DNA methyltransferase M. Hha I in a ternary complex with DNA and AdoMet in solution. Methylation involves addition of the Cys81 sulfhydryl anion to the 6-position of Cyt18, followed by a nucleophilic attack of the resultant carbanion at C5 on the AdoMet methyl group. It was found in this simulation that the distances between the sulfhydryl group (SG) of Cys81 to the C6 of Cyt18 (SG-C6) and methyl carbon (CH3) of AdoMet to the C5 of cytosine (CH3-C5) are dependent on the dihedral angle chi (O4'-C1'-N1-C2) of the nucleotide. When the chi angle of Cyt18 is low (< -80 degrees), the SG-C6 and CH3-C5 distances are large. A high chi angle (> -80 degrees) for the target cytosine residue reduces the distances for both SG-C6 and CH3-C5, and the angles formed between the cytosine ring and AdoMet correspond well to values for the transition state structures formed during methylation of cytosine from ab initio calculations. Two possible proton sources for protonation of N3 of the cytosine residue upon formation of the covalent intermediate were found in the simulation. The protonated amine group of AdoMet could provide a proton via a water bridge, or Arg163 could also be the source of the proton for N3 via a water bridge. The simulation provides insights into how the H5 of cytosine could go from the active site into solvent. Conserved residues Asn304 and Gln82 stabilize a water network within the active site of M. Hha I which provides a route for H5 to diffuse into bulk solvent. An initially distant water molecule was able to diffuse into the active site of the enzyme and replace a position of a crystallographic water molecule in close proximity to the C5 of cytosine. The movement of this water molecule showed that a channel exists between Gln82 and the AdoMet in M. Hha I which allows both water and protons to easily gain access to the active site of the enzyme.
Copyright 1999 Academic Press.
Similar articles
- S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation.
Youngblood B, Shieh FK, Buller F, Bullock T, Reich NO. Youngblood B, et al. Biochemistry. 2007 Jul 31;46(30):8766-75. doi: 10.1021/bi7005948. Epub 2007 Jul 7. Biochemistry. 2007. PMID: 17616174 - Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.
Sheikhnejad G, Brank A, Christman JK, Goddard A, Alvarez E, Ford H Jr, Marquez VE, Marasco CJ, Sufrin JR, O'gara M, Cheng X. Sheikhnejad G, et al. J Mol Biol. 1999 Feb 5;285(5):2021-34. doi: 10.1006/jmbi.1998.2426. J Mol Biol. 1999. PMID: 9925782 - AdoMet-dependent methyl-transfer: Glu119 is essential for DNA C5-cytosine methyltransferase M.HhaI.
Shieh FK, Reich NO. Shieh FK, et al. J Mol Biol. 2007 Nov 9;373(5):1157-68. doi: 10.1016/j.jmb.2007.08.009. Epub 2007 Aug 19. J Mol Biol. 2007. PMID: 17897676 - Molecular recognition motifs in cytidinium and 2'-deoxycytidinium salts with composite anions.
Gilski M, Jaskólski M. Gilski M, et al. Acta Biochim Pol. 1998;45(4):917-28. Acta Biochim Pol. 1998. PMID: 10397339 Review. - Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites.
Marquez VE, Wang P, Nicklaus MC, Maier M, Manoharan M, Christman JK, Banavali NK, Mackerell AD Jr. Marquez VE, et al. Nucleosides Nucleotides Nucleic Acids. 2001 Apr-Jul;20(4-7):451-9. doi: 10.1081/NCN-100002319. Nucleosides Nucleotides Nucleic Acids. 2001. PMID: 11563060 Review.
Cited by
- Molecular and enzymatic profiles of mammalian DNA methyltransferases: structures and targets for drugs.
Xu F, Mao C, Ding Y, Rui C, Wu L, Shi A, Zhang H, Zhang L, Xu Z. Xu F, et al. Curr Med Chem. 2010;17(33):4052-71. doi: 10.2174/092986710793205372. Curr Med Chem. 2010. PMID: 20939822 Free PMC article. Review. - A theoretical examination of the factors controlling the catalytic efficiency of the DNA-(adenine-N6)-methyltransferase from Thermus aquaticus.
Newby ZE, Lau EY, Bruice TC. Newby ZE, et al. Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7922-7. doi: 10.1073/pnas.122231499. Proc Natl Acad Sci U S A. 2002. PMID: 12060740 Free PMC article. - Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations.
Liu L, Shi T, Houk KN, Zhao YL. Liu L, et al. RSC Adv. 2019 Oct 3;9(54):31425-31434. doi: 10.1039/c9ra06791d. eCollection 2019 Oct 1. RSC Adv. 2019. PMID: 35527972 Free PMC article. - Methyltransferase-directed derivatization of 5-hydroxymethylcytosine in DNA.
Liutkevičiūtė Z, Kriukienė E, Grigaitytė I, Masevičius V, Klimašauskas S. Liutkevičiūtė Z, et al. Angew Chem Int Ed Engl. 2011 Feb 25;50(9):2090-3. doi: 10.1002/anie.201007169. Epub 2011 Jan 26. Angew Chem Int Ed Engl. 2011. PMID: 21344558 Free PMC article. - Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.
Luo J, Bruice TC. Luo J, et al. Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16194-8. doi: 10.1073/pnas.0507913102. Epub 2005 Oct 19. Proc Natl Acad Sci U S A. 2005. PMID: 16236720 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases
Miscellaneous