Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.
Prokaryotic DNA methyltransferase M.SssI recognizes and methylates C5 position of the cytosine residue within the CG dinucleotides in DNA. It is an excellent model for studying the mechanism of interaction between CG-specific eukaryotic methyltransferases and DNA. We have built a structural model of M.SssI in complex with the substrate DNA and its analogues as well as the cofactor analogue S-adenosyl-L-homocysteine (AdoHcy) using the previously solved structures of M.HhaI and M.HaeIII as templates. The model was constructed according to the recently developed "FRankenstein's monster" approach. Based on the model, amino acid residues taking part in cofactor binding, target recognition and catalysis were predicted. We also modeled covalent modification of the DNA substrate and studied its influence on protein-DNA interactions.
Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia.
E V
EV
Koudan
J M
JM
Bujnicki
E S
ES
Gromova
D015075:2-Aminopurine / Q000737:chemistry; D000595:Amino Acid Sequence; D004247:DNA / Q000737:chemistry*; D015257:DNA-Cytosine Methylases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009700:Nucleoside Deaminases / Q000737:chemistry*; D010649:Phenylalanine / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013149:Spiroplasma / Q000201:enzymology
D015075:2-Aminopurine; D010649:Phenylalanine; D004247:DNA; C081573:DNA modification methylase SssI; D015257:DNA-Cytosine Methylases; D009700:Nucleoside Deaminases; C062075:S-adenosylhomocysteine deaminase