page_title: Retroviral ribonuclease H
section_title: Structure
hierarchical_section_title: Retroviral ribonuclease H / Structure
caption_attribution_description: English: The structure of the HIV reverse transcriptase (RT) heterodimer in complex with an RNA:DNA duplex. The reverse transcriptase p66 fragment is shown in yellow with the C-terminal RNase H domain shown in blue (active site residues in magenta spheres). The orange strand is RNA and the red strand is DNA. The p51 fragment - a differently processed protein equivalent to p66 without the RNase H domain - is shown in green. Rendered from PDB 1HYS. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. Sarafianos, S.G., Das, K., Tantillo, C., Clark Jr., A.D., Ding, J., Whitcomb, J.M., Boyer, P.L., Hughes, S.H., Arnold, E. (2001) EMBO J. 20: 1449-1461 PubMed: 11250910 PubMedCentral: PMC145536 DOI: 10.1093/emboj/20.6.1449
context_page_description: The retroviral ribonuclease H is a catalytic domain of the retroviral reverse transcriptase enzyme. The RT enzyme is used to generate complementary DNA from the retroviral RNA genome. This process is called reverse transcription. To complete this complex process, the retroviral RT enzymes need to adopt a multifunctional nature. They therefore possess 3 of the following biochemical activities: RNA-dependent DNA polymerase, ribonuclease H, and DNA-dependent DNA polymerase activities. Like all RNase H enzymes, the retroviral RNase H domain cleaves DNA/RNA duplexes and will not degrade DNA or unhybridized RNA.
context_section_description: Although the RT structures from human, murine and avian retroviruses display different subunits, the relative sizes, orientation and connection of the DNA polymerase and RNase H domains are strikingly similar. The RNase H domain occupies ~25% of the RT protein C-terminal. The DNA polymerase domain occupies ~55% of the RT protein N-terminal.
  The RNase H domains of MMLV and HIV-1 RT enzymes are structural very similar to the Escherichia coli and Bacillus halodurans RNases H as well as to human RNaseH1. In general, the folded structures of retroviral RNase H domains take the form of 5-stranded mixed beta sheets flanked by four alpha helices in an asymmetric distribution. A notable difference between the various RNase H proteins is the presence or absence of the C-helix (present in E. coli, MLV and human RNases H, absent in HIV-1, B. halodurans and ASLV RNases H), a positively charged alpha helix also referred to as the basic loop or protrusion. It is believed to have a role in substrate binding.
caption: The crystal structure of the HIV reverse transcriptase heterodimer (yellow and green), with the RNase H domain shown in blue (active site in magenta spheres). The orange nucleic acid strand is RNA, the red strand is DNA.[4]
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