Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins
This family includes two different GIY-YIG enzymes, coliphage T4 non-specific endonuclease II (EndoII), and type II restriction endonuclease R.Hpy188I. They display high sequence similarity to each other, and both of them contain an extra N-terminal hairpin that lacks counterparts in other GIY-YIG enzymes. EndoII encoded by gene denA catalyzes the initial step in degradation of host DNA, which permits scavenging of host-derived nucleotides for phage DNA synthesis. R.Hpy188I recognizes the unique sequence, 5'-TCNGA-3', and cleaves the DNA between nucleotides N and G in its recognition sequence to generate a single nucleotide 3'-overhang. EndoII binds to two DNA substrates as an X-shaped tetrameric structure composed as a dimer of dimers. In contrast, two subunits of R.Hpy188I form a dimer to embrace one bound DNA. Divalent metal-ion cofactors are required for their catalytic events, but not for the substrates binding.
Comment:Type II restriction endonuclease R. Hpy188I (3OQG) has similar core structure with that of coliphage T4 endonuclease II (2WSH) but exhibits an unusual active site.
Structure:3OQG; active site among the substrate complex of type II restriction endonuclease R. Hpy188I
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