Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BgIII DNA sequence

The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BgIII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BgIII-like. We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT). We find the complex to be more BgIII-like with similarities mapping to DNA conformation, domain organization, and residues involved in catalysis. However, BstYI is unique in containing an extended arm subdomain, and the mechanism of DNA capture has both BgIII-like and BamHI-like elements. Further, DNA recognition is more minimal than BgIII and BamHI, where only two residues mediate recognition of the entire core sequence. Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes.