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. DpnM, and by extension the DpnM family or group alpha Mtases, contains the consensus fold and AdoMet-binding motifs found in most Mtases. Structural considerations suggest that macromolecular Mtases evolved from small-molecule Mtases, with different groups of DNA Mtases evolving independently. Mtases may have evolved from dehydrogenases. Comparison of these enzymes indicates that in protein evolution, the structural fold is most highly conserved, then function and lastly sequence.

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The two DNA-adenine methylases encoded by the Dpn II restriction gene cassette were purified, and their activities were compared on various DNA substrates. DpnA was able to methylate single-strand DNA and double-strand DNA, whereas DpnM methylated only double-strand DNA.

The structural gene (dpnM) for the Dpn H DNA methylase of Streptococcus pneumoniae, which is part of the Dpn H restriction system and methylates adenine in the sequence 5'-G-A-T-C-3', was identified by subcloning fragments of a chromosomal segment from a Dpn 11-producing strain in an S. pneumonwae host/vector cloning system and demonstrating function of the gene also in Bacillus subtilis. Determination of the nucleotide sequence of the gene and adjacent DNA indicates that it encodes a polypeptide of 32,903 daltons. A putative promoter for transcription of the gene lies within a hundred nucleotides of the polypeptide start codon.Comparison of the coding sequence to that of the dam gene of Escherichia coli, which encodes a similar methylase, revealed 30% of the amino acid residues in the two enzymes to be identical. This homology presumably reflects a common origin of the two genes prior to the divergence of Gram-positive and Gram-negative bacteria. It is suggested that the restriction function of the gene is primitive, and that the homologous restriction system in E. cofl has evolved to play an accessory role in heteroduplex DNA base mismatch repair.Strains of Streptococcus pneumoniae contain one of two complementary and incompatible restriction systems (1, 2). Some strains contain the endonuclease Dpn I, which is unusual in that it acts only on the methylated DNA sequence 5'-G-m6A-T-C-3' (3,4); the DNA in these strains is not methylated at this site. Other strains contain the complementary endonuclease Dpn II, which acts only on unmethylated 5'-G-A-T-C-3' sites (4, 5). The latter strains contain a DNA methylase that methylates adenine at these sites. The genes for the Dpn II DNA methylase and endonuclease appear to be linked because they are simultaneously transferred in bacterial transformation by chromosomal DNA (2).A segment of chromosomal DNA that expresses the Dpn II DNA methylase, but not the endonuclease, was recently cloned in the S. pneumoniae/pMP5 host/vector system (6). The recombinant plasmid containing the methylase gene could be transferred to a Dpn I-containing strain only when expression of Dpn I was turned off by a mechanism as yet unknown (7). In the present work the gene encoding the methylase was identified, and its nucleotide sequence was determined. The DNA sequence adjacent to the structural gene was also examined to explore possible mechanisms controlling its expression. A likely promoter for its transcription was identified.The dam gene (8) of Escherichia coli encodes a methylase with the same specificity as the Dpn II methylase (4). The nucleotide sequence of the dam gene was recently determined (9), and it was of interest to compare the amino acid sequences deduced for the two polypeptides of similar function but different origin. Despite the considerable evolutionary divergence of the source bacteria, one being Grampositive and the other Gram-negative, significant homology was detected between the protein products of their chromosomally located methylase genes. The apparently ...