The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry

Abstract

The type I restriction and modification (R-M) enzyme from Salmonella enterica serovar kaduna (StySKI) recognises the DNA sequence 5'-CGAT(N)7GTTA, an unusual target for a type I R-M system in that it comprises two tetranucltranucleotide components. The amino target recognition domain (TRD) of StySKI recognises 5'-CGAT and shows 36% amino acid identity with the carboxy TRD of EcoR1241 which recognises the complementary, but degenerate, sequence 5'-RTCG. Current models predict that the amino and carboxy TRDs of the specificity subunit are in inverted orientations within a structure with 2-fold rotational symmetry. The complementary target sequences recognised by the amino TRD of StySKI and the carboxy TRD of EcoR1241 are consistent with the predicted inverted positions of the TRDs. Amino TRDs of similar amino acid sequence have been shown to recognise the same nucleotide sequence. The similarity reported here, the first example of one between amino and carboxy TRDs, while consistent with a conserved mechanism of target recognition, offers additional flexibility in the evolution of sequence specificity by increasing the potential diversity of DNA targets for a given number of TRDs. StySKI identifies the first member of the IB family in Salmonella species.