InterPro domain: IPR044730

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 Escherichia coli is the best characterised [ 1 , 2 , 3 ]. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus 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 Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H [ 4 ]. 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.

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 3.1.26.4 catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids.

The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [ 5 , 6 , 7 , 8 ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ 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 [ 9 ]. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences.

This domain is found predominantly in plants, including the putative ribonuclease H protein At1g65750 from Arabidopsis.

1. Folding the ribonuclease H domain of Moloney murine leukemia virus reverse transcriptase requires metal binding or a short N-terminal extension. Proteins 33, 135-43
2. Ribonuclease H. FEBS J. 276, 1481
3. Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site. J. Biol. Chem. 276, 7266-71
4. Sequence and comparative structural analysis of the murine leukaemia virus amphotropic strain 4070A RNase H domain. Arch. Virol. 144, 2185-99
5. Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Science 249, 1398-405
6. Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site. Proteins 17, 337-46
7. Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase. Science 252, 88-95
8. Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol. Cell 28, 264-76