InterPro domain: IPR023160

This superfamily represents the helix-loop-helix cap domain of ribonuclease HII. This C-terminal domain forms a compact structure consisting of two alpha-helices: alpha 8 and alpha 9. Unlike the N-terminal domain, bacterial RNases HI do not possess this domain. In the full-length enzyme, the alpha9 helix is followed by 15 amino acid residues, of which conformation is likely to be flexible, as revealed from the susceptibility to trypsin digestion. It has been suggested that this domain confers substrate-specific binding capacity to the core nuclease architecture, thus accounting for the endonucleolytic specificity of the type 2 RNase H family members [ 1 ]. It also has been suggested that this domain to be involved in the interaction with the DNA/RNA hybrid [ 2 ].

1. Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication. J. Mol. Biol. 307, 541-56
2. Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses. Protein Sci. 10, 707-14