PROTEIN-NUCLEIC ACID INTERACTIONS AND DNA CONFORMATION IN A COMPLEX OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 REVERSE-TRANSCRIPTASE WITH A DOUBLE-STRANDED DNA TEMPLATE-PRIMER

The conformation of the DNA and the interactions of the nucleic acid w ith the protein in a complex of human immunodeficiency virus type 1 (H IV-1) reverse transcriptase (RT) and a 19-mer/18-mer double-stranded D NA template-primer (dsDNA) are described. The structure of this HIV-1 RT complex with dsDNA selves as a useful paradigm for studying aspects of nucleotide polymerases such as catalysis, fidelity, drug inhibitio n, and drug resistance. The bound dsDNA has a bend of approximately 41 degrees at the junction of an A-form region (first-five base pairs ne ar the polymerase active site) and a B-form region (the last nine base pairs toward the RNase H active sire). The 41 degrees bend occurs smo othly over the four base pairs between the A-form portion and the B-fo rm portion in the vicinity of helices alpha H and alpha I of the p66 t humb subdomain. The inter actions between the dsDNA and protein primar ily involve the sugar-phosphate backbone of the nucleic acid and struc tural elements of the palm, thumb, and RNase H of p66, and are not seq uence specific. Amino acid residues from the polymerase active site re gion, including amino acid residues of the conserved Sr-Met-Asp-Asp (Y MDD) motif and the ''primer grip,'' interact with 3'-terminal nucleoti des of the primer str-and and are involved in positioning the primer t erminal nucleotide and its 3'-OH group at the polymerase active site. Amino acid residues of the ''template grip'' have close contacts with the template strand and aid in positioning the template strand near th e polymerase active site. Helix alpha H of the p66 thumb is partly ins erted into the minor groove of the dsDNA and helix alpha I is directly adjacent to the backbone of the template strand. Amino acid residues of beta 1', alpha A', alpha B', and the loop containing His539 of the RNase H domain interact with the primer strand of the dsDNA. (C) 1997 John Wiley & Sons, Inc.