A Full-Coordinate Model of the Polymerase Domain of HIV-I Reverse Transcriptase and its Interaction With a Nucleic Acid Substrate

Abstract

We present a full-coordinate model of residues 1–319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320–6324 (1993)) which is currently available to the degree of C- coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, Mol. Biol. 218, 183–194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

Two magnesium ions were placed in the active site in order to better understand the polymerization mechanism. The positions of metal ions in a number of structures guided the placement of ions in this study (L.S. Beese and T.A. Steitz, EMBO. J10, 25–33 (1991); T.A. Steitz and J.A. Steitz, P.N.A.S. USA 90, 6498–6502 (1993); D.L. Sloan et al., J. Biol. Chem. 250, 8913–8920 (1975); R.F. Setlik et al., J. Biomol. Str. Dyn. 10, 945–972 (1993)). The geometry of the active site allowed metal ions to be bound to Asp 110 and Asp 186 of the catalytic triad. However, due to spacial constraints, Asp 185 was found unable to bind to a metal ion. Due to its proximity to the attacking 3′OH group of the 3′ terminal residue of the primer strand, it is proposed that this residue acts as a general base which abstracts a proton from the attacking group. Based on the locations of these metal ions with respect to the attacking group of the 3′ end of the primer strand and to an incoming dTTP placed in the active site, we propose roles for the magnesium ions and discuss a mechanism through which chain elongation occurs. Also reported are the interactions between the polymerase domain and the template-primer complex observed in our model. These interactions are discussed in view of their possible roles in positioning the nucleic acid complex in the binding cleft and in regard to other structural and functional roles. The importance of these residues as observed in our model is compared to results from multiple sequence alignments and various mutational studies on HIV-I reverse transcriptase.