VI. HhaI DNA Methyltransferase Complexed with DNA and AdoMet Click here to see HhaI DNA Methyltransferase structure when complexed with DNA and AdoMet. HhaI DNA methyltransferase 1MHTMarz is a m5c-methyltransferase that recognizes the. 5'-GCGC-3' sequence in double stranded DNA DNA binding Zn finger motifs pyrimidine, purine bases G,C,G,C between double strands of DNA . < > DNA binds to HhaI methyltransferase in the binding cleft formed by the three domains and is situated so that the major groove faces the small domain and the minor groove faces the large domain. There are three sites of protein/DNA interaction: two glycine rich loops in the small domain and the active site loop in the large domain < >. The HhaI monomer conformation is altered by DNA binding. This change brings the active site loop towards the binding cleft, where it contacts the minor groove of DNA and binds in three places < >. The binding of DNA also brings the small domain closer to the binding cleft so that the glycine rich loops can come into contact with the major groove of the DNA molecule < >. In order for the HhaI molecule to methylate the cytosine base, the DNA must undergo structural distortions. Commonly, structural distortions caused by DNA binding proteins result in DNA bends. These proteins usually contact the surface of bases in the major or minor grooves and interact with the external, phosphodiester backbone. In the case of HhaI, however, the buried atoms of cytosine bases of DNA must be accessible for methylation chemistry, requiring drastic distortions to make the bases accessible to the methyltransferase. The phosphodiester backbone of DNA is distorted in such a manner that the phosphates on either side of the target cytosine are shifted outward, increasing the distance between the phosphates on the two strands of DNA. The shifting of the phosphates allows the target cytosine to flip out of the DNA helix through the minor groove < >. Once out of the helix, the target cytosine is held in place by three conserved motifs surrounding the binding cleft in the large domain using hydrogen bonds and salt bridges < >. A simple removal of the target cytosine would be enrgetically unfavorable, and two residues located on two separate loops move into the helix to occupy the position vacated by the target cytosine, thus restoring stacking interactions < >. These residues are unique to HhaI methyltransferase. The conformational changes bring the target cytosine, the catalytic nucleophile of the active site loop (cysteine81), and the methyl donor (AdoMet) into close proximity < >. VII. Fresh replicate DNA methylase DNMT1 PDB 3PT6 The DNA methyltransferase DNMT1, shown here from PDB entry 3PT6, as DNA is being replicated, adds the proper methyl groups to the new DNA strands C. Methyl groups are almost always added to Cytosine bases with the sequence: ---CG--- ---GC--- that both strands have a Cytosine, so in a methylated region of DNA, both strands will have a methyl group. When the DNA is replicated, each of the new DNA double helices will have one old strand, complete with methyl groups, and one new strand, which is not methylated. So, DNMT1 just needs to look for CG base steps where only one strand has a methyl group and DNMT1 add to second strand C methyl group. De novo methylation ensures that only hemimethylated CpG dinucleotides gain access to the active site. Genomic methylation patterns in mammals is required for monoallelic expression of imprinted genes, for the transcriptional silencing of retrotransposon, and for X chromosome inactivation in females. Structural overview of mDNMT1(646-1602) DNA 19 bp nucleotide oligomer complex with bound AdoHcy. (Fig. 1a, b) DNMT1(646-1600) DNA methyltransferase 3PT6Marz , 3PTAMarz , 4DA4Marz , 4DKJMarz , 3MHTMarz is a m5c-methyltransferase that recognizes the. 5'-GCGG-3' sequence in double stranded DNA DNA binding Zn finger motifs pyrimidine, purine bases G,C,G,G . (Fig. 2a, b) The conserved Zn finger 3PT6Zn651-699 Zn 2 Coordinative Bond between residues Cys656,Cys659,Cys662,Cys694 Zn 4 Coordinative Bond between residues Cys667,Cys670,Cys673,Cys689 is indicated as yellow stick. The conserved Zn finger 3PTAZn651-699 Zn 2 Coordinative Bond between residues Cys653Cys656Cys659Cys691 Zn 5 Coordinative Bond between residues Cys664,Cys667,Cys670,Cys686 is indicated as yellow stick. The conserved Zn finger 4DA4Zn1477-1506 The conserved Zn finger4DA4Zn794-902 Zn 1702 Coordinative Bond between residues CYS1479,CYS1481,CYS1487,HIS1504 Zn 1703 Coordinative Bond between residues HIS796,CYS823,CYS897,CYS900 is indicated as yellow stick. References 1. Cheng, X., Kumar, S., Posfai,P.,Pflugrath, J., Roberts, R.(1993). Crystal Structure of the HhaI DNA Methyltransferase Complexed with S-Adenosyl-L-Methionine. Cell. 74:299-307. PDB:1MHT 2. Klimasauskas, S., Kumar, S., Roberts, R., Cheng, X.(1994). HhaI Methyltransferase Flips Its Target Base Out of the DNA Helix. Cell. 76: 357-369.PDB:1MHT 3 . Nature. 2007 September 13; 449(7159): 248–251. DNA DNMT3 Methylase PDB: 2QRV 4 . Science 25 February 2011: Vol. 331 no. 6020 pp. 1036-1040 DNA DNMT1 Methylase PDB:3PT6,3PTA 5 . July 2011 Molecule of the Month by David Goodsell PDB DNA Methyltransferases HhaI Methylase PDB: 2QRV,3PT6 1MHT=DNA=DNMT3,DNMT1 6 . PNAS 2011: vol. 108 no. 22 mouse3PT6+DNA+3PTAhuman; 3AV4; Hha1 5mht;1MHT;AdoHcy 3PT9 DMT1 7. Science 10 February 2012: Vol. 335 no. 6069 pp. 709-712 PDB: 4DA4,3PT6,3PTA,3MHT,4DKJ