A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase (pol) domain of the 66-kilodalton subunit has a large cleft analogous to that of the Klenow fragment of Escherichia coli DNA polymerase I. However, the 51-kilodalton subunit of identical sequence has no such cleft because the four subdomains of the pol domain occupy completely different relative positions. Two of the four pol subdomains appear to be structurally related to subdomains of the Klenow fragment, including one containing the catalytic site. The subdomain that appears likely to bind the template strand at the pol active site has a different structure in the two polymerases. Duplex A-form RNA-DNA hybrid can be model-built into the cleft that runs between the ribonuclease H and pol active sites. Nevirapine is almost completely buried in a pocket near but not overlapping with the pol active site. Residues whose mutation results in drug resistance have been approximately located.

The dipyridodiazepinone Nevirapine is a potent and highly specific inhibitor of the reverse transcriptase (RT) from human immunodeficiency virus type 1 (HIV-1). It is a member of an important class of nonnucleoside drugs that appear to share part or all of the same binding site on the enzyme but are susceptible to a variety of spontaneous drugresistance mutations. The co-crystal-structure of HIV-1 RT

The reverse transcriptase from human immunodeficiency virus type 1 is a heterodimer consisting of one 66-kDa and one 51-kDa subunit. The p66 subunit Perhaps the most surprising aspect of the structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is the observation that the polymerase domain assumes a different structure in the two subunits in spite of having the same polypeptide chain sequence (1). HIV-1 RT consists of one 66-kDa polypeptide chain (p66) consisting of a polymerase domain and an RNase H domain and one 51-kDa polypeptide chain (p51) containing only the polymerase domain. These two subunits interact asymmetrically to generate only one polymerase cleft that binds one primer-template, one dNTP, one noncompetitive inhibitor, and one tRNA (2-5). The polymerase domains of p51 and p66 differ by having an alternative arrangement of four subdomains (1). The three subdomains that form the large polymerase active-site cleft in p66 are called "fingers," "thumb," and "palm" by analogy ofthis polymerase structure to that ofa right hand. The fourth subdomain is called "connection" because it lies between the polymerase and RNase H active sites in p66. Although the heterodimer is the most stable dimer, with an equilibrium dissociation constant (Kd) of =1 x 10-9 M (6, 7), both p66 and p51 homodimers have been observed in vitro but are much less tightly associated (7). The major question addressed here is how a single amino acid sequence can form two quite different structures and result in such an asymmetric subunit interaction. Furthermore, and in the light of the structural observations, it is of interest to consider the likely conformation of pSi or p66 monomers as well as the possible structures of homodimers of these subunits.The crystal structure of the HIV-1 RT heterodimer complexed with a noncompetitive inhibitor, Nevirapine, was initially derived from a 3.5-A resolution electron density map (1) and has now been partially refined at 2.9-A resolution (8, 9). The structure of HIV-1 RT complexed with the Fab portion of a monoclonal antibody and duplex DNA determined at 3-A resolution shows the same structure for the RT and provides experimental evidence for the primer-template location (10). RESULTS AND DISCUSSIONThe Asymmetric Dimer Structure. The four polymerase subdomains of HIV-1 RT have very different relative orientations in the two subunits ofthe RT heterodimer (Fig. 1). The p51 subunit has a compact structure that we can refer to as "closed," while the p66 subunit has a more extended structure and a large cleft that can be referred to as "open." With the connection domains oriented identically, the different sets of interactions made by the fingers, palm, and thumb subdomains of each ofthe two subunits are clearly seen (Fig. 1). Changes in the contacts between the connection and the fingers subdomains are more modest.Interactions between the two subunits are completely asymmetric in that the subunit interface on p51 involves different amino acid residues than the...