Ribonuclease H (RNase H) (EC 3.1.26.4) recognizes and cleaves the RNA strand of RNA-DNA heteroduplexes.

In prokaryotes RNase H is involved in removing the RNA of RNA-DNA hybrids, particularly the primers of Okazaki fragments in lagging-strand DNA synthesis [1]. An additional function of the bacterial RNase H domain is to generate primers for initiation of DNA replication [2].

The RNase H domain is also present in retroviral reverse transcriptase proteins where it performs three functions : (a) generation of a polypurine tract which acts as the primer for plus strand DNA synthesis, (b) removal of RNA primers from nascent minus and plus DNA strands, and (c) degradation of the original RNA template. For HIV, inactivation of the RNase H renders the virus non-infectious, making this enzymatic activity a target for therapy of AIDS [1].

In eukaryotes, the RNase H1 protein is present in nuclei, but it has also been isolated from mitochondria of many organisms. In mouse inactivation of the RNaseH1 gene arrest development about day E8.5 because of a failure to generate mtDNA, indicating an essential role for RNase H1 during mammalian embryogenesis [3].

The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved (see for example <PDB:1RNH>) [4,5,6]. All have four β strands and four to five α helices. The Escherichia coli RNase H1 protein binds a single Mg(2+) ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 [5]. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences.

The profile we developed covers the whole RNase H domain.