Abstract
Using a computer-assisted molecular modeling protocol, we have completed the three-dimensional structures of HIV-1 reverse transcriptase and the Klenow fragment of DNA polymerase I based on the C alpha crystal coordinates of the individual enzymes. The two model-built structures were then used to compare the electrostatic potential contours and analyze the spatial positions of residues conserved in the catalytic domains of the two enzymes. In spite of rather weak sequence similarity and different folding patterns between the DNA-dependent DNA polymerase (pol I) and the RNA-dependent DNA polymerases (RT), we have noted the occurrence of identical or similar residues at common spatial positions in pol I and RT in a three-dimensional context. The homologous residues present at equivalent spatial position in the Klenow fragment and the p66 subunit of HIV-1 RT may therefore imply their functional similarity. Furthermore, these conserved residues may represent a similar structure-function feature in all polymerases.
Highlights
Using a computer-assisted molecular modeling protJoa-cobo-Molina et al, 1993).The secondary structures of various col,wehavecompletedthethree-dimensionalstrucshort segmentsof the two polypeptides are the same in twheo tures of HIV-1 reverse transcriptase and the Klenow subunits
Crystal contains motif C, has shown a common spatial framework for structure studies (Kohlstaedet al., 1992; Jacobo-Molina et al, the catalytically important triad of carboxyl groups (Asp-882, 1993; reviewed by Nanni et al, 1993) have confirmed the Glu-883, and Asp-705 in Klenow; Asp-185, Asp-186, and Asppresence of structurallysimilar three-dimensional motifs 110 in HIV-1 RT). The positions of these ibnoth RT and theKlenow fragment three residues are conserved in the multiple sequence alignof DNA polymerase I, the subunict omposition ment of all polymerases (Delarue et al, 1990)
The crystal structure analysis, thpoelymerase domains of both and theKlenow fragment arenow available, we compared the the p66 and the p51 subunitsof HIV-1 RT consist of identical spatial positions of all highly conserved residues in the polyprimary aminoacid sequence but theirfolding patterns or spa- merase domain, using the Cct position of carboxyl triad as a tial arrangements are quitedifferent
Summary
Structures of the Klenow Fragmenatnd H N - 1 RT-For the structure of HIV-1RT, two different crystal structure Ca coordinates were obtained from the ProteinData Bank (PDB) (PDB file1HLT Kohlstaedt et al, 1992; PDBfile 1HMI: Jacobo-Molinaet al., 1993).We began with the Ca coordinates of two crystalsby aligning their RNaseH domains. Electrostatic Potential Calcu1ations"lb assess the possible similarity in theDNA-binding environmentin Klenow fragment and HIV-1 RT, we have calculated the electrostatic potential of the modeled structures of the twoenzymes.Fig. 3 gives a qualitative idea of positive and negative electrostatic potential regions in Klenow and HIV-1RT. As seen, both enzymesexhibit electropositivepotential contoursin a similar fashion. The positive potential appear to comspond well with the DNA duplex-bindingregion reported in thecrystal structures of the two enzymes (Beeseet al., 1993; Jacobo-Molina eat l., 1993). Nosignificant similarity in the residues was observed in theregion of duplex DNA binding
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