page_title: Retroviral ribonuclease H
section_title: Structure
hierarchical_section_title: Retroviral ribonuclease H / Structure
caption_attribution_description: English: The ribonuclease H domain from the HIV-1 reverse transcriptase protein (blue), with the four active-site carboxylate residues shown in magenta. The domain is superposed on the ribonuclease HI domain from Escherichia coli (tan). Rendered from PDB 3K2P (HIV) and 2RN2 (E. coli). Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site. Himmel, D.M., Maegley, K.A., Pauly, T.A., Bauman, J.D., Das, K., Dharia, C., Clark, A.D., Ryan, K., Hickey, M.J., Love, R.A., Hughes, S.H., Bergqvist, S., Arnold, E. (2009) Structure 17: 1625-1635 PubMed: 20004166 PubMedCentral: PMC3365588 DOI: 10.1016/j.str.2009.09.016 Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Nakamura, H., Ikehara, M., Matsuzaki, T., Morikawa, K. (1992) J.Mol.Biol. 223: 1029-1052 PubMed: 1311386
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 ribonuclease H domain from the HIV-1 reverse transcriptase protein (blue), with the four active-site carboxylate residues shown in magenta.[1] The domain is superposed on the ribonuclease HI domain from Escherichia coli (tan), illustrating the presence of the C-helix and basic protrusion in the E. coli homolog.[3]
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