A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate.
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, J. 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.
Setlik
R F
RF
Department of Biophysics, Roswell Park Cancer Institute, Buffalo, New York 14263.
Meyer
D J
DJ
Shibata
M
M
Roskwitalski
R
R
Ornstein
R L
RL
Rein
R
R
D000595:Amino Acid Sequence; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D054303:HIV Reverse Transcriptase; D015497:HIV-1 / Q000737:chemistry* / Q000201:enzymology; D008274:Magnesium / Q000502:physiology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009696:Nucleic Acids / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry*; D016415:Sequence Alignment; D013379:Substrate Specificity
D009696:Nucleic Acids; D054303:HIV Reverse Transcriptase; D012194:RNA-Directed DNA Polymerase; D004259:DNA-Directed DNA Polymerase; D008274:Magnesium