4DKJ

CpG specific methyltransferase in complex with target DNA

Summary for 4DKJ

• Entry DOI: 10.2210/pdb4dkj/pdb
• Related: 1MHT 2C7P 3PT6 3PT9 3PTA 4DA4
• Descriptor: Cytosine-specific methyltransferase, DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)-3'), DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3'), ... (6 entities in total)
• Functional Keywords: cg-specificity, dna intercalation, cpg sequence, cytosine c5-methylation, c5-methylcytosine, nucleotide flipping, s-adenosyl-l-methionine-dependent methyltransferases, c-5 cytosine-specific dna methylases, dna (cytosine-5-)-methyltransferase activity, dna binding, dna (cytosine-5-)-methylation, intracellular, transferase-dna complex, transferase/dna
• Biological source: Mycoplasma penetrans
• Total number of polymer chains: 3
• Total formula weight: 56380.19

Authors

Wojciechowski, M.,Czapinska, H.,Bochtler, M. (deposition date: 2012-02-03, release date: 2012-12-05, Last modification date: 2023-09-13)

Primary citation

Wojciechowski, M.,Czapinska, H.,Bochtler, M.
CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
Proc.Natl.Acad.Sci.USA, 110:105-110, 2013

PubMed Abstract: Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively expressed or phase variable CpG-specific DNA methyltransferases. The very CpG poor Mycoplasma penetrans and its constitutively active CpG-specific methyltransferase M.MpeI were chosen for further characterization. Genome-wide sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target sites both in vivo and in vitro in a locus-nonselective manner. A crystal structure of M.MpeI with DNA at 2.15-Å resolution showed that the substrate base was flipped and that its place in the DNA stack was taken by a glutamine residue. A phenylalanine residue was intercalated into the "weak" CpG step of the nonsubstrate strand, indicating mechanistic similarities in the recognition of the short CpG target sequence by prokaryotic and eukaryotic DNA methyltransferases.

PubMed: 23248272
DOI: 10.1073/pnas.1207986110

Experimental method

X-RAY DIFFRACTION (2.15 Å)