STRUCTURE OF UNLIGANDED HIV-1 REVERSE-TRANSCRIPTASE AT 2.7 ANGSTROM RESOLUTION - IMPLICATIONS OF CONFORMATIONAL-CHANGES FOR POLYMERIZATION AND INHIBITION MECHANISMS

Background: HIV-1 reverse transcriptase (RT) is a major target for ant i-HIV drugs. A considerable amount of information about the structure of RT is available, both unliganded and in complex with template-prime r or nonnucleoside RT inhibitors (NNRTIs), But significant conformatio nal differences in the p66 polymerase domain among the unliganded stru ctures have complicated the interpretation of these data, leading to d ifferent proposals for the mechanisms of polymerization and inhibition , Results: We report the structure of an unliganded RT at 2.7 Angstrom resolution, crystallized in space group C2 with a crystal packing sim ilar to that of the RT-NNRTI complexes. The p66 thumb subdomain is fol ded into the DNA-binding cleft, Comparison of the unliganded RT struct ures with the DNA-bound RT and the NNRTI-bound RT structures reveals t hat the p66 thumb subdomain can exhibit two different upright conforma tions. In the DNA-bound RT, the p66 thumb subdomain adopts an upright position that can be described as resulting from a rigid-body rotation of the p66 thumb along the 'thumb's knuckle' located near residues Tr p239 (in strand beta 14) and Val317 (in beta 15) compared with the thu mb position in the unliganded RT structure. NNRTI binding induces an a dditional hinge movement of the p66 thumb near the thumb's knuckle, ca using the p66 thumb to adopt a configuration that is even more extende d than in the DNA-bound RT structure, Conclusions: The p66 thumb subdo main is extremely flexible, NNRTI binding induces both short-range and long-range structural distortions in several domains of RT, which are expected to alter the position and conformation of the template-prime r. These changes may account for the inhibition of polymerization and the alteration of the cleavage specificity of RNase H by NNRTI binding .