Crystal Structure of the HIV-1 Integrase Catalytic Core and C-Terminal Domains: A Model for Viral DNA Binding

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 97; no. 15; pp. 8233 - 8238
• Main Authors: Julian C.-H. Chen, Krucinski, Jolanta, Larry J. W. Miercke, Finer-Moore, Janet S., Tang, Ann H., Leavitt, Andrew D., Stroud, Robert M.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences of the United States of America 18.07.2000; National Acad Sciences; National Academy of Sciences; The National Academy of Sciences
• Subjects: Active sites; Amino Acid Sequence; Animals; Biological Sciences; Catalytic Domain; Cell Line; Crystal structure; Crystallography, X-Ray; Crystals; Dimers; DNA; DNA - metabolism; HIV 1; HIV Integrase - chemistry; HIV Integrase - genetics; HIV Integrase - metabolism; Human immunodeficiency virus 1; Humans; integrase; Models, Biological; Models, Molecular; Molecular Sequence Data; Monomers; Mutagenesis, Site-Directed; Protein Binding; Protein Conformation; Proteins; Sequence Homology, Amino Acid; Solubility; Viral DNA
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.150220297

Insolubility of full-length HIV-1 integrase (IN) limited previous structure analyses to individual domains. By introducing five point mutations, we engineered a more soluble IN that allowed us to generate multidomain HIV-1 IN crystals. The first multidomain HIV-1 IN structure is reported. It incorporates the catalytic core and C-terminal domains (residues 52-288). The structure resolved to 2.8 angstrom is a Y-shaped dimer. Within the dimer, the catalytic core domains form the only dimer interface, and the C-terminal domains are located 55 angstrom apart. A 26-aa α -helix, α 6, links the C-terminal domain to the catalytic core. A kink in one of the two α 6 helices occurs near a known proteolytic site, suggesting that it may act as a flexible elbow to reorient the domains during the integration process. Two proteins that bind DNA in a sequence-independent manner are structurally homologous to the HIV-1 IN C-terminal domain, suggesting a similar protein-DNA interaction in which the IN C-terminal domain may serve to bind, bend, and orient viral DNA during integration. A strip of positively charged amino acids contributed by both monomers emerges from each active site of the dimer, suggesting a minimally dimeric platform for binding each viral DNA end. The crystal structure of the isolated catalytic core domain (residues 52-210), independently determined at 1.6- angstrom resolution, is identical to the core domain within the two-domain 52-288 structure.