Type I restriction-modification (R-M) enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. They recognize bipartite DNA sequences of 2-4 consecutive bases. The two target recognition domains (TRDs) within a single S-subunit provide a background for this recognition. Two M-subunits and a single S-subunit can form a separate oligomeric protein from the holo R-M complex and function as a methyltransferase (MTase). Here, we show the crystal structure of the intact MTase from Vibrio vulnificus in complex with the DNA-mimicking Ocr protein. This intact MTase includes regions for an M-subunit and a half S (S1/2)-subunit in a single polypeptide. The canonical M-subunit domain structure in the N-terminus is followed by the S1/2-subunit of a long a-helix, a TRD, and another long a-helix. Unexpectedly, the two a-helices of the S1/2-subunit associate to form a coiled-coil structure that further ensembles with those of the neighboring molecule in the crystalline state and in solution. The TRD cleft of the S1/2-subunit and the M-domain of the neighboring molecule form a cleft binding for the Ocr protein. Structure and interpretation of the biophysical data indicate the dynamic character of the protein to form the DNA-binding sites by two molecules with the four-helical bundle as an assembling point. The revealed molecular features of the intact MS1/2 structure provides how the phage evades its killing system in bacteria.