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Human Immunodeficiency Virus Reverse Transcriptase pp 53–75Cite as

The RNase H Domain: Structure, Function and Mechanism

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Abstract

An essential step of proliferation of retroviruses and transposition of long terminal repeat-containing retrotransposons is conversion of their single-stranded RNA genome into integration-competent, double-stranded proviral DNA by the multifunctional reverse transcriptase (RT) (Gilboa et al. 1979). RT is an enzyme with two activities. RNA-dependent DNA polymerase activity is first used to synthesize minus (−) strand DNA from the positive-stranded RNA genome, resulting in an RNA/DNA replication intermediate. The RNA strand of these hybrids is degraded by the RNase H activity to allow DNA-dependent synthesis of (+) strand DNA. RNase H activity is used not only to nonspecifically remove the RNA but also to specifically generate and remove RNA primers required to initiate synthesis of both DNA strands. In this chapter, we describe the current understanding of the HIV RNase H domain and its cellular counterparts – RNases H1 – with particular focus on structural data which, together with biochemical and computational studies, have revealed a detailed picture of the mechanism of action of this important and clinically significant enzyme. We will also discuss how the RNase H domain functions in the context of the dimeric HIV-1 RT.

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References

  • Arion D et al (2002) Mutational analysis of Tyr-501 of HIV-1 reverse transcriptase. Effects on ribonuclease H activity and inhibition of this activity by N-acylhydrazones. J Biol Chem 277(2):1370–1374

    PubMed  CAS  Google Scholar 

  • Arudchandran A et al (2000) The absence of ribonuclease H1 or H2 alters the sensitivity of Saccharomyces cerevisiae to hydroxyurea, caffeine and ethyl methanesulphonate: implications for roles of RNases H in DNA replication and repair. Genes Cells 5(10):789–802

    PubMed  CAS  Google Scholar 

  • Beilhartz GL et al (2009) HIV-1 reverse transcriptase can simultaneously engage its DNA/RNA substrate at both DNA polymerase and RNase H active sites: implications for RNase H inhibition. J Mol Biol 388(3):462–474

    PubMed  CAS  Google Scholar 

  • Ben-Artzi H et al (1992) Characterization of the double stranded RNA dependent RNase activity associated with recombinant reverse transcriptases. Nucleic Acids Res 20(19): 5115–5118

    PubMed  CAS  Google Scholar 

  • Boyer PL, Ferris AL, Hughes SH (1992a) Cassette mutagenesis of the reverse transcriptase of human immunodeficiency virus type 1. J Virol 66(2):1031–1039

    PubMed  CAS  Google Scholar 

  • Boyer PL, Ferris AL, Hughes SH (1992b) Mutational analysis of the fingers domain of human immunodeficiency virus type 1 reverse transcriptase. J Virol 66(12):7533–7537

    PubMed  CAS  Google Scholar 

  • Boyer PL et al (1994) Mutational analysis of the fingers and palm subdomains of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase. J Mol Biol 243(3):472–483

    PubMed  CAS  Google Scholar 

  • Broccoli S et al (2004) Effects of RNA polymerase modifications on transcription-induced negative supercoiling and associated R-loop formation. Mol Microbiol 52(6):1769–1779

    PubMed  CAS  Google Scholar 

  • Cerritelli SM et al (1998) A common 40 amino acid motif in eukaryotic RNases H1 and caulimovirus ORF VI proteins binds to duplex RNAs. Nucleic Acids Res 26(7):1834–1840

    PubMed  CAS  Google Scholar 

  • Cerritelli SM et al (2003) Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice. Mol Cell 11(3):807–815

    PubMed  CAS  Google Scholar 

  • Chung S et al (2011) Synthesis, activity, and structural analysis of novel alpha-hydroxytropolone inhibitors of human immunodeficiency virus reverse transcriptase-associated ribonuclease H. J Med Chem 54(13):4462–4473

    PubMed  CAS  Google Scholar 

  • Cirino NM et al (1995) Divalent cation modulation of the ribonuclease functions of human immunodeficiency virus reverse transcriptase. Biochemistry 34(31):9936–9943

    PubMed  CAS  Google Scholar 

  • Cote ML, Roth MJ (2008) Murine leukemia virus reverse transcriptase: structural comparison with HIV-1 reverse transcriptase. Virus Res 134(1–2):186–202

    PubMed  CAS  Google Scholar 

  • Davies JF 2nd et al (1991) Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase. Science 252(5002):88–95

    PubMed  CAS  Google Scholar 

  • De Vivo M, Dal Peraro M, Klein ML (2008) Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism. J Am Chem Soc 130(33):10955–10962

    PubMed  Google Scholar 

  • DeStefano JJ et al (1991) Polymerization and RNase H activities of the reverse transcriptases from avian myeloblastosis, human immunodeficiency, and Moloney murine leukemia viruses are functionally uncoupled. J Biol Chem 266(12):7423–7431

    PubMed  CAS  Google Scholar 

  • DeStefano JJ et al (1994) Quantitative analysis of RNA cleavage during RNA-directed DNA synthesis by human immunodeficiency and avian myeloblastosis virus reverse transcriptases. Nucleic Acids Res 22(18):3793–3800

    PubMed  CAS  Google Scholar 

  • DeStefano JJ et al (2001) Physical mapping of HIV reverse transcriptase to the 5′ end of RNA primers. J Biol Chem 276(35):32515–32521

    PubMed  CAS  Google Scholar 

  • Drolet M et al (1995) Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I. Proc Natl Acad Sci USA 92(8):3526–3530

    PubMed  CAS  Google Scholar 

  • Dudding LR, Nkabinde NC, Mizrahi V (1991) Analysis of the RNA- and DNA-dependent DNA polymerase activities of point mutants of HIV-1 reverse transcriptase lacking ribonuclease H activity. Biochemistry 30(43):10498–10506

    PubMed  CAS  Google Scholar 

  • Elsasser B, Fels G (2010) Atomistic details of the associative phosphodiester cleavage in human ribonuclease H. Phys Chem Chem Phys 12(36):11081–11088

    PubMed  Google Scholar 

  • Evans DB et al (1991) A recombinant ribonuclease H domain of HIV-1 reverse transcriptase that is enzymatically active. J Biol Chem 266(31):20583–20585

    PubMed  CAS  Google Scholar 

  • Fuentes GM et al (1995) Use of an oligoribonucleotide containing the polypurine tract sequence as a primer by HIV reverse transcriptase. J Biol Chem 270(47):28169–28176

    PubMed  CAS  Google Scholar 

  • Furfine ES, Reardon JE (1991a) Reverse transcriptase. RNase H from the human immunodeficiency virus. Relationship of the DNA polymerase and RNA hydrolysis activities. J Biol Chem 266(1):406–412

    PubMed  CAS  Google Scholar 

  • Furfine ES, Reardon JE (1991b) Human immunodeficiency virus reverse transcriptase ribonuclease H: specificity of tRNA(Lys3)-primer excision. Biochemistry 30(29):7041–7046

    PubMed  CAS  Google Scholar 

  • Gaidamakov SA et al (2005) Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain. Nucleic Acids Res 33(7):2166–2175

    PubMed  CAS  Google Scholar 

  • Gao HQ et al (1998) Effects of mutations in the polymerase domain on the polymerase, RNase H and strand transfer activities of human immunodeficiency virus type 1 reverse transcriptase. J Mol Biol 277(3):559–572

    PubMed  CAS  Google Scholar 

  • Gao L et al (2008) Apparent defects in processive DNA synthesis, strand transfer, and primer elongation of Met-184 mutants of HIV-1 reverse transcriptase derive solely from a dNTP utilization defect. J Biol Chem 283(14):9196–9205

    PubMed  CAS  Google Scholar 

  • Gilboa E et al (1979) A detailed model of reverse transcription and tests of crucial aspects. Cell 18(1):93–100

    PubMed  CAS  Google Scholar 

  • Goedken ER, Marqusee S (2001) Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site. J Biol Chem 276(10):7266–7271

    PubMed  CAS  Google Scholar 

  • Gopalakrishnan V, Peliska JA, Benkovic SJ (1992) Human immunodeficiency virus type 1 reverse transcriptase: spatial and temporal relationship between the polymerase and RNase H activities. Proc Natl Acad Sci USA 89(22):10763–10767

    PubMed  CAS  Google Scholar 

  • Gotte M et al (1998) Localization of the active site of HIV-1 reverse transcriptase-associated RNase H domain on a DNA template using site-specific generated hydroxyl radicals. J Biol Chem 273(17):10139–10146

    PubMed  CAS  Google Scholar 

  • Gotte M et al (1999) Temporal coordination between initiation of HIV (+)-strand DNA synthesis and primer removal. J Biol Chem 274(16):11159–11169

    PubMed  CAS  Google Scholar 

  • Hansen J, Schulze T, Moelling K (1987) RNase H activity associated with bacterially expressed reverse transcriptase of human T-cell lymphotropic virus III/lymphadenopathy-associated virus. J Biol Chem 262(26):12393–12396

    PubMed  CAS  Google Scholar 

  • Hansen J et al (1988) Identification and characterization of HIV-specific RNase H by monoclonal antibody. EMBO J 7(1):239–243

    PubMed  CAS  Google Scholar 

  • Haruki M et al (1994) Investigating the role of conserved residue Asp134 in Escherichia coli ribonuclease HI by site-directed random mutagenesis. Eur J Biochem 220(2):623–631

    PubMed  CAS  Google Scholar 

  • Haruki M et al (1997) Kinetic and stoichiometric analysis for the binding of Escherichia coli ribonuclease HI to RNA-DNA hybrids using surface plasmon resonance. J Biol Chem 272(35):22015–22022

    PubMed  CAS  Google Scholar 

  • Haruki M et al (2000) Catalysis by Escherichia coli ribonuclease HI is facilitated by a phosphate group of the substrate. Biochemistry 39(45):13939–13944

    PubMed  CAS  Google Scholar 

  • Himmel DM et al (2009) Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site. Structure 17(12):1625–1635

    PubMed  CAS  Google Scholar 

  • Hostomsky Z et al (1991) Reconstitution in vitro of RNase H activity by using purified N-terminal and C-terminal domains of human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci USA 88(4):1148–1152

    PubMed  CAS  Google Scholar 

  • Hostomsky Z et al (1994) Redesignation of the RNase D activity associated with retroviral reverse transcriptase as RNase H. J Virol 68(3):1970–1971

    PubMed  CAS  Google Scholar 

  • Huang H et al (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282(5394):1669–1675

    PubMed  CAS  Google Scholar 

  • Huber HE, Richardson CC (1990) Processing of the primer for plus strand DNA synthesis by human immunodeficiency virus 1 reverse transcriptase. J Biol Chem 265(18):10565–10573

    PubMed  CAS  Google Scholar 

  • Jacobo-Molina A et al (1993) Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. Proc Natl Acad Sci USA 90(13):6320–6324

    PubMed  CAS  Google Scholar 

  • Julias JG et al (2002) Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo. Proc Natl Acad Sci USA 99(14):9515–9520

    PubMed  CAS  Google Scholar 

  • Julias JG et al (2003) Mutation of amino acids in the connection domain of human immunodeficiency virus type 1 reverse transcriptase that contact the template-primer affects RNase H activity. J Virol 77(15):8548–8554

    PubMed  CAS  Google Scholar 

  • Kanaya S (1998) Enzymatic activity and protein stability of E. coli ribonuclease HI. In: Toulme JJ, Crouch HRJ (eds) Ribonucleases. INSERM, Paris, pp.1–38

    Google Scholar 

  • Kanaya S et al (1990) Identification of the amino acid residues involved in an active site of Escherichia coli ribonuclease H by site-directed mutagenesis. J Biol Chem 265(8):4615–4621

    PubMed  CAS  Google Scholar 

  • Kanaya S, Katsuda-Nakai C, Ikehara M (1991) Importance of the positive charge cluster in Escherichia coli ribonuclease HI for the effective binding of the substrate. J Biol Chem 266(18):11621–11627

    PubMed  CAS  Google Scholar 

  • Katayanagi K et al (1990) Three-dimensional structure of ribonuclease H from E. coli. Nature 347(6290):306–309

    PubMed  CAS  Google Scholar 

  • Kati WM et al (1992) Mechanism and fidelity of HIV reverse transcriptase. J Biol Chem 267(36):25988–25997

    PubMed  CAS  Google Scholar 

  • Keck JL, Marqusee S (1995) Substitution of a highly basic helix/loop sequence into the RNase H domain of human immunodeficiency virus reverse transcriptase restores its Mn(2+)-dependent RNase H activity. Proc Natl Acad Sci USA 92(7):2740–2744

    PubMed  CAS  Google Scholar 

  • Keck JL, Marqusee S (1996) The putative substrate recognition loop of Escherichia coli ribonuclease H is not essential for activity. J Biol Chem 271(33):19883–19887

    PubMed  CAS  Google Scholar 

  • Keck JL, Goedken ER, Marqusee S (1998) Activation/attenuation model for RNase H. A one-metal mechanism with second-metal inhibition. J Biol Chem 273(51):34128–34133

    PubMed  CAS  Google Scholar 

  • Krakowiak A et al (2002) Stereochemical course of Escherichia coli RNase H. Chembiochem 3(12):1242–1250

    PubMed  CAS  Google Scholar 

  • Krug MS, Berger SL (1989) Ribonuclease H activities associated with viral reverse transcriptases are endonucleases. Proc Natl Acad Sci USA 86(10):3539–3543

    PubMed  CAS  Google Scholar 

  • Kvaratskhelia M, Budihas SR, Le Grice SF (2002) Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase. J Biol Chem 277(19): 16689–16696

    PubMed  CAS  Google Scholar 

  • Lapkouski et al (2013) Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation. Nat Struct Mol Biol 20(2):230–236

    Google Scholar 

  • Lazzaro F et al (2012) RNase H and postreplication repair protect cells from Ribonucleotides incorporated in DNA. Mol Cell 45(1):99–110

    PubMed  CAS  Google Scholar 

  • Lim D, Orlova M, Goff SP (2002) Mutations of the RNase H C helix of the Moloney murine leukemia virus reverse transcriptase reveal defects in polypurine tract recognition. J Virol 76(16):8360–8373

    PubMed  CAS  Google Scholar 

  • Lima WF et al (2007a) Human RNase H1 discriminates between subtle variations in the structure of the heteroduplex substrate. Mol Pharmacol 71(1):83–91

    PubMed  CAS  Google Scholar 

  • Lima WF et al (2007b) The positional influence of the helical geometry of the heteroduplex substrate on human RNase H1 catalysis. Mol Pharmacol 71(1):73–82

    PubMed  CAS  Google Scholar 

  • Mandal D et al (2006) Analysis of HIV-1 replication block due to substitutions at F61 residue of reverse transcriptase reveals additional defects involving the RNase H function. Nucleic Acids Res 34(10):2853–2863

    PubMed  CAS  Google Scholar 

  • McWilliams MJ et al (2003) Mutations in the 5′ end of the human immunodeficiency virus type 1 polypurine tract affect RNase H cleavage specificity and virus titer. J Virol 77(20): 11150–11157

    PubMed  CAS  Google Scholar 

  • McWilliams MJ et al (2006) Combining mutations in HIV-1 reverse transcriptase with mutations in the HIV-1 polypurine tract affects RNase H cleavages involved in PPT utilization. Virology 348(2):378–388

    PubMed  CAS  Google Scholar 

  • Miller HI, Riggs AD, Gill GN (1973) Ribonuclease H (hybrid) in Escherichia coli. Identification and characterization. J Biol Chem 248(7):2621–2624

    PubMed  CAS  Google Scholar 

  • Mizrahi V et al (1990) Site-directed mutagenesis of the conserved Asp-443 and Asp-498 carboxy-terminal residues of HIV-1 reverse transcriptase. Nucleic Acids Res 18(18): 5359–5363

    PubMed  CAS  Google Scholar 

  • Mizrahi V, Brooksbank RL, Nkabinde NC (1994) Mutagenesis of the conserved aspartic acid 443, glutamic acid 478, asparagine 494, and aspartic acid 498 residues in the ribonuclease H domain of p66/p51 human immunodeficiency virus type I reverse transcriptase. Expression and biochemical analysis. J Biol Chem 269(30):19245–19249

    PubMed  CAS  Google Scholar 

  • Nowak E et al (2013) Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874–3887

    Google Scholar 

  • Nowotny M (2009) Retroviral integrase superfamily: the structural perspective. EMBO Rep 10(2):144–151

    PubMed  CAS  Google Scholar 

  • Nowotny M, Yang W (2006) Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J 25(9):1924–1933

    PubMed  CAS  Google Scholar 

  • Nowotny M et al (2005) Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121(7):1005–1016

    PubMed  CAS  Google Scholar 

  • Nowotny M et al (2007) Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol Cell 28(2):264–276

    PubMed  CAS  Google Scholar 

  • Nowotny M et al (2008) Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD. EMBO J 27(7):1172–1181

    PubMed  CAS  Google Scholar 

  • Oda Y, Yoshida M, Kanaya S (1993) Role of histidine 124 in the catalytic function of ribonuclease HI from Escherichia coli. J Biol Chem 268(1):88–92

    PubMed  CAS  Google Scholar 

  • Ohtani N et al (1999a) Molecular diversities of RNases H. J Biosci Bioeng 88(1):12–19

    PubMed  CAS  Google Scholar 

  • Ohtani N et al (1999b) Identification of the genes encoding Mn2+−dependent RNase HII and Mg2+−dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families. Biochemistry 38(2):605–618

    PubMed  CAS  Google Scholar 

  • Palaniappan C et al (1996) Helix structure and ends of RNA/DNA hybrids direct the cleavage specificity of HIV-1 reverse transcriptase RNase H. J Biol Chem 271(4):2063–2070

    PubMed  CAS  Google Scholar 

  • Palaniappan C et al (1998) Control of initiation of viral plus strand DNA synthesis by HIV reverse transcriptase. J Biol Chem 273(7):3808–3816

    PubMed  CAS  Google Scholar 

  • Pallan PS, Egli M (2008) Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex. Cell Cycle 7(16): 2562–2569

    PubMed  CAS  Google Scholar 

  • Peliska JA, Benkovic SJ (1992) Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science 258(5085):1112–1118

    PubMed  CAS  Google Scholar 

  • Powell MD, Levin JG (1996) Sequence and structural determinants required for priming of plus-strand DNA synthesis by the human immunodeficiency virus type 1 polypurine tract. J Virol 70(8):5288–5296

    PubMed  CAS  Google Scholar 

  • Powell MD et al (1999) Residues in the alphaH and alphaI helices of the HIV-1 reverse transcriptase thumb subdomain required for the specificity of RNase H-catalyzed removal of the polypurine tract primer. J Biol Chem 274(28):19885–19893

    PubMed  CAS  Google Scholar 

  • Pullen KA, Ishimoto LK, Champoux JJ (1992) Incomplete removal of the RNA primer for minus-strand DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase. J Virol 66(1):367–373

    PubMed  CAS  Google Scholar 

  • Purohit V et al (2007) Mechanisms that prevent template inactivation by HIV-1 reverse transcriptase RNase H cleavages. J Biol Chem 282(17):12598–12609

    PubMed  CAS  Google Scholar 

  • Rausch JW, Le Grice SF (1997) Substituting a conserved residue of the ribonuclease H domain alters substrate hydrolysis by retroviral reverse transcriptase. J Biol Chem 272(13):8602–8610

    PubMed  CAS  Google Scholar 

  • Rausch JW, Le Grice SF (2004) ‘Binding, bending and bonding’: polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int J Biochem Cell Biol 36(9):1752–1766

    PubMed  CAS  Google Scholar 

  • Rausch JW et al (2002) Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity. Biochemistry 41(15):4856–4865

    PubMed  CAS  Google Scholar 

  • Rausch JW et al (2003) Hydrolysis of RNA/DNA hybrids containing nonpolar pyrimidine isosteres defines regions essential for HIV type 1 polypurine tract selection. Proc Natl Acad Sci USA 100(20):11279–11284

    PubMed  CAS  Google Scholar 

  • Rosta E et al (2011) Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc 133(23):8934–8941

    PubMed  CAS  Google Scholar 

  • Sarafianos SG et al (2001) Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J 20(6):1449–1461

    PubMed  CAS  Google Scholar 

  • Schatz O et al (1989) Point mutations in conserved amino acid residues within the C-terminal domain of HIV-1 reverse transcriptase specifically repress RNase H function. FEBS Lett 257(2):311–314

    PubMed  CAS  Google Scholar 

  • Schultz SJ, Champoux JJ (1996) RNase H domain of Moloney murine leukemia virus reverse transcriptase retains activity but requires the polymerase domain for specificity. J Virol 70(12):8630–8638

    PubMed  CAS  Google Scholar 

  • Schultz SJ, Champoux JJ (2008) RNase H activity: structure, specificity, and function in reverse transcription. Virus Res 134(1–2):86–103

    PubMed  CAS  Google Scholar 

  • Schultz SJ, Zhang M, Champoux JJ (2004) Recognition of internal cleavage sites by retroviral RNases H. J Mol Biol 344(3):635–652

    PubMed  CAS  Google Scholar 

  • Schultz SJ, Zhang M, Champoux JJ (2006) Sequence, distance, and accessibility are determinants of 5′-end-directed cleavages by retroviral RNases H. J Biol Chem 281(4):1943–1955

    PubMed  CAS  Google Scholar 

  • Smith JS, Roth MJ (1993) Purification and characterization of an active human immunodeficiency virus type 1 RNase H domain. J Virol 67(7):4037–4049

    PubMed  CAS  Google Scholar 

  • Smith JS, Gritsman K, Roth MJ (1994) Contributions of DNA polymerase subdomains to the RNase H activity of human immunodeficiency virus type 1 reverse transcriptase. J Virol 68(9):5721–5729

    PubMed  CAS  Google Scholar 

  • Smith CM, Smith JS, Roth MJ (1999) RNase H requirements for the second strand transfer reaction of human immunodeficiency virus type 1 reverse transcription. J Virol 73(8):6573–6581

    PubMed  CAS  Google Scholar 

  • Stahl SJ et al (1994) Construction of an enzymatically active ribonuclease H domain of human immunodeficiency virus type 1 reverse transcriptase. Protein Eng 7(9):1103–1108

    PubMed  CAS  Google Scholar 

  • Starnes MC, Cheng YC (1989) Human immunodeficiency virus reverse transcriptase-associated RNase H activity. J Biol Chem 264(12):7073–7077

    PubMed  CAS  Google Scholar 

  • Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90(14):6498–6502

    PubMed  CAS  Google Scholar 

  • Suo Z, Johnson KA (1997) Effect of RNA secondary structure on RNA cleavage catalyzed by HIV-1 reverse transcriptase. Biochemistry 36(41):12468–12476

    PubMed  CAS  Google Scholar 

  • Tanese N, Goff SP (1988) Domain structure of the Moloney murine leukemia virus reverse transcriptase: mutational analysis and separate expression of the DNA polymerase and RNase H activities. Proc Natl Acad Sci USA 85(6):1777–1781

    PubMed  CAS  Google Scholar 

  • Telesnitsky A, Blain SW, Goff SP (1992) Defects in Moloney murine leukemia virus replication caused by a reverse transcriptase mutation modeled on the structure of Escherichia coli RNase H. J Virol 66(2):615–622

    PubMed  CAS  Google Scholar 

  • Tisdale M et al (1991) Mutations within the RNase H domain of human immunodeficiency virus type 1 reverse transcriptase abolish virus infectivity. J Gen Virol 72(Pt 1):59–66

    PubMed  CAS  Google Scholar 

  • Volkmann S et al (1993) Enzymatic analysis of two HIV-1 reverse transcriptase mutants with mutations in carboxyl-terminal amino acid residues conserved among retroviral ribonucleases H. J Biol Chem 268(4):2674–2683

    PubMed  CAS  Google Scholar 

  • Wahba L et al (2011) RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability. Mol Cell 44(6):978–988

    PubMed  CAS  Google Scholar 

  • Wang J et al (1994) Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer. Proc Natl Acad Sci USA 91(15):7242–7246

    PubMed  CAS  Google Scholar 

  • Wisniewski M et al (2000a) Unique progressive cleavage mechanism of HIV reverse transcriptase RNase H. Proc Natl Acad Sci USA 97(22):11978–11983

    PubMed  CAS  Google Scholar 

  • Wisniewski M et al (2000b) The sequential mechanism of HIV reverse transcriptase RNase H. J Biol Chem 275(48):37664–37671

    PubMed  CAS  Google Scholar 

  • Wisniewski M et al (2002) Substrate requirements for secondary cleavage by HIV-1 reverse transcriptase RNase H. J Biol Chem 277(32):28400–28410

    PubMed  CAS  Google Scholar 

  • Wohrl BM, Moelling K (1990) Interaction of HIV-1 ribonuclease H with polypurine tract containing RNA-DNA hybrids. Biochemistry 29(44):10141–10147

    PubMed  CAS  Google Scholar 

  • Yang W et al (1990) Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Science 249(4975):1398–1405

    PubMed  CAS  Google Scholar 

  • Yang W, Lee JY, Nowotny M (2006) Making and breaking nucleic acids: two-Mg2+−ion catalysis and substrate specificity. Mol Cell 22(1):5–13

    PubMed  CAS  Google Scholar 

  • Zhan X, Crouch RJ (1997) The isolated RNase H domain of murine leukemia virus reverse transcriptase. Retention of activity with concomitant loss of specificity. J Biol Chem 272(35): 22023–22029

    PubMed  CAS  Google Scholar 

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  1. International Institute of Molecular and Cell Biology, Warsaw, Poland

    Marcin Nowotny & Małgorzata Figiel

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  1. Marcin Nowotny
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Correspondence to Marcin Nowotny .

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  1. , HIV Drug Resistance Program, National Cancer Institute, Frederick, 21702, Maryland, USA

    Stuart LeGrice

  2. McGill University, 3775 University Street 3755, Montreal, H3T 1E2, Québec, Canada

    Matthias Gotte

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Nowotny, M., Figiel, M. (2013). The RNase H Domain: Structure, Function and Mechanism. In: LeGrice, S., Gotte, M. (eds) Human Immunodeficiency Virus Reverse Transcriptase. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7291-9_3

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