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RNase H activity: structure, specificity, and function in reverse transcription Schultz SJ; Champoux JJVirus Res 2008[Jun]; 134 (1-2): 86-103This review compares the well-studied RNase H activities of human immunodeficiency virus, type 1 (HIV-1) and Moloney murine leukemia virus (MoMLV) reverse transcriptases. The RNase H domains of HIV-1 and MoMLV are structurally very similar, with functions assigned to conserved subregions like the RNase H primer grip and the connection subdomain, as well as to distinct features like the C-helix and loop in MoMLV RNase H. Like cellular RNases H, catalysis by the retroviral enzymes appears to involve a two-metal ion mechanism. Unlike cellular RNases H, the retroviral RNases H display three different modes of cleavage: internal, DNA 3' end-directed, and RNA 5' end-directed. All three modes of cleavage appear to have roles in reverse transcription. Nucleotide sequence is an important determinant of cleavage specificity with both enzymes exhibiting a preference for specific nucleotides at discrete positions flanking an internal cleavage site as well as during tRNA primer removal and plus-strand primer generation. RNA 5' end-directed and DNA 3' end-directed cleavages show similar sequence preferences at the positions closest to a cleavage site. A model for how RNase H selects cleavage sites is presented that incorporates both sequence preferences and the concept of a defined window for allowable cleavage from a recessed end. Finally, the RNase H activity of HIV-1 is considered as a target for anti-virals as well as a participant in drug resistance.|*Reverse Transcription/drug effects[MESH]|Amino Acid Sequence[MESH]|Base Sequence[MESH]|Crystallography, X-Ray[MESH]|HIV Infections/drug therapy/enzymology[MESH]|HIV-1/*chemistry/drug effects/*enzymology/genetics[MESH]|Humans[MESH]|Moloney murine leukemia virus/*chemistry/drug effects/*enzymology/genetics[MESH]|Protein Structure, Secondary[MESH]|Protein Structure, Tertiary[MESH]|RNA-Directed DNA Polymerase/*chemistry/genetics/*metabolism[MESH]|Reverse Transcriptase Inhibitors/pharmacology[MESH]|Ribonuclease H/antagonists & inhibitors/*chemistry/genetics/*metabolism[MESH]|Substrate Specificity[MESH] |
