<p>The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from <taxon tax_id="562">Escherichia coli</taxon> is the best characterised [<cite idref="PUB00006422"/>]. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as <taxon tax_id="11886">Rous sarcoma virus</taxon> and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of <taxon tax_id="11676">Human immunodeficiency virus 1</taxon> (HIV-1) reverse transcriptase and in E. coli RNase H [<cite idref="PUB00006461"/>]. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities.</p><p>Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H <db_xref db="EC" dbkey="3.1.26.4"/> catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. </p><p>The 3D structure of the RNase H domain from diverse bacteria and retroviruseshas been solved [<cite idref="PUB00015351"/>, <cite idref="PUB00015352"/>, <cite idref="PUB00015353"/>]. All have four betastrands and four to five alpha helices. The E. coli RNase H1 proteinbinds a single Mg2+ ion cofactor in the active site of the enzyme. Thedivalent cation is bound by the carboxyl groups of four acidic residues,Asp-10, Glu-48, Asp-70, and Asp-134 [<cite idref="PUB00015352"/>]. The first three acidic residues arehighly conserved in all bacterial and retroviral RNase H sequences.</p>