Catalytic GIY-YIG domain of type II restriction enzyme R.Eco29kI, R.NgoMIII, and similar proteins
This family corresponds to the catalytic GIY-YIG domain of GGCGCC-specific type II restriction endonucleases R.Eco29kI, NgoMIII, and similar proteins. R.Eco29kI is encoded on plasmid pECO29 in the E. coli strain 29K. This enzyme recognizes the palindromic 5'-CCGC/GG-3' target and cuts between Cyt4 and Gua5 on each strand of the restriction site to generate 3'-staggered ends. R.Eco29kI forms a domain-swapped homodimeric catalytically active complex during DNA binding and cleavage. Each subunit contains one GIY-YIG catalytic motif. Restriction endonucleases R.NgoMIII is an isoschizomer of R.Eco29kI. Members in this family are single-domain proteins sharing sequence similarities with the catalytic domain of GIY-YIG endonucleases, such as homing endonuclease I-TevI. However, they utilize loop insertions and terminal extensions instead of the separate DNA-binding domain to interact with the target site 5'-CCGC/GG-3'. A divalent metal-ion cofactor is required for their catalysis, but not for their substrate binding.
Jiyao W et al.(2023). "The conserved domain database in 2023.",