title: Structure of HIV-1 reverse transcriptase/DNA complex at 7 A resolution showing active site locations.
abstract: AIDS, caused by human immunodeficiency virus (HIV), is one of the world's most serious health problems, with current protocols being inadequate for either prevention or successful long-term treatment. In retroviruses such as HIV, the enzyme reverse transcriptase copies the single-stranded RNA genome into double-stranded DNA that is then integrated into the chromosomes of infected cells. Reverse transcriptase is the target of the most widely used treatments for AIDS, 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxyinosine (ddI), but resistant strains of HIV-1 arise in patients after a relatively short time. There are several nonnucleoside inhibitors of HIV-1 reverse transcriptase, but resistance to such agents also develops rapidly. We report here the structure at 7 A resolution of a ternary complex of the HIV-1 reverse transcriptase heterodimer, a monoclonal antibody Fab fragment, and a duplex DNA template-primer. The double-stranded DNA binds in a groove on the surface of the enzyme. The electron density near one end of the DNA matches well with the known structure of the HIV-1 reverse transcriptase RNase H domain. At the opposite end of the DNA, a mercurated derivative of UTP has been localized by difference Fourier methods, allowing tentative identification of the polymerase nucleoside triphosphate binding site. We also determined the structure of the reverse transcriptase/Fab complex in the absence of template-primer to compare the bound and free forms of the enzyme. The presence of DNA correlates with movement of protein electron density in the vicinity of the putative template-primer binding groove. These results have important implications for developing improved inhibitors of reverse transcriptase for the treatment of AIDS.
authors.affiliation: Center for Advanced Biotechnology and Medicine (CABM), Piscataway, New Jersey 08854-5638.
authors.forename: E
authors.initials: E
authors.lastname: Arnold
authors.forename: A
authors.initials: A
authors.lastname: Jacobo-Molina
authors.forename: R G
authors.initials: RG
authors.lastname: Nanni
authors.forename: R L
authors.initials: RL
authors.lastname: Williams
authors.forename: X
authors.initials: X
authors.lastname: Lu
authors.forename: J
authors.initials: J
authors.lastname: Ding
authors.forename: A D
authors.initials: AD
authors.lastname: Clark
authors.forename: A
authors.initials: A
authors.lastname: Zhang
authors.forename: A L
authors.initials: AL
authors.lastname: Ferris
authors.forename: P
authors.initials: P
authors.lastname: Clark
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D003460:Crystallization; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry*; D054303:HIV Reverse Transcriptase; D015497:HIV-1 / Q000201:enzymology*; D007140:Immunoglobulin Fab Fragments; D008767:Methylmercury Compounds; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009941:Organomercury Compounds; D011487:Protein Conformation; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry*; D013329:Structure-Activity Relationship; D014544:Uridine Triphosphate / Q000031:analogs & derivatives; D014961:X-Ray Diffraction
chemical_list: D004268:DNA-Binding Proteins; D007140:Immunoglobulin Fab Fragments; D008767:Methylmercury Compounds; D009941:Organomercury Compounds; C016782:tetrakis(acetoxymercuri)methane; C035548:5'-mercuriuridine triphosphate; D004247:DNA; D054303:HIV Reverse Transcriptase; D012194:RNA-Directed DNA Polymerase; D014544:Uridine Triphosphate