A FULL-COORDINATE MODEL OF THE POLYMERASE DOMAIN OF HIV-I REVERSE-TRANSCRIPTASE AND ITS INTERACTION WITH A NUCLEIC-ACID SUBSTRATE

We present a full-coordinate model of residues 1 - 319 of the polymera se domain of HIV-I reverse transcriptase. This model was constructed f rom the x-ray crystallographic structure of Jacobo-Molina et al. (Jaco bo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currentl y available to the degree of C-coordinates. The backbone and side-chai n atoms were constructed using the MAXSPROUT suite of programs (L. Hol m and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined throug h molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer compl ex. 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.