X-ray structure of simian immunodeficiency virus integrase containing the core and C-terminal domain (residues 50-293) - An initial glance of the viral DNA binding platform

The crystal structure of simian immunodeficiency virus (SIV) integrase that contains in a single polypeptide the core and the C-terminal deoxyoligonuc leotide binding domain has been determined at 3 Angstrom resolution with an X-value of 0.203 in the space group P2(1)2(1)2(1). Four integrase core dom ains and one C-terminal domain are found to be well defined in the asymmetr ic unit. The segment extending from residues 114 to 121 assumes the same po sition as seen in the integrase core domain of avian sarcoma virus as well as human immunodeficiency virus type-1 (HIV-1) crystallized in the absence of sodium cacodylate. The flexible loop in the active site, composed of res idues 141-151, remains incompletely defined, but the location of the essent ial Glu152 residue is unambiguous. The residues from 210-218 that Link the core and C-terminal domains can be traced as an extension from the core wit h a short gap at residues 214-215. The C-alpha folding of the C-terminal do main is similar to the solution structure of this domain from HIV-1 integra se. However, the dimeric form seen in the NMR structure cannot exist as rel ated by the non-crystallographic symmetry in the SIV integrase crystal. The two flexible loops of the C-terminal domain, residues 228-236 and residues 244-249, are much better fixed in the crystal structure than in the NMR st ructure with the former in the immediate vicinity of the flexible loop of t he core domain. The interface between the two domains encompasses a solvent -exclusion area of 1500 Angstrom(2). Residues from both domains purportedly involved in DNA binding are narrowly distributed on the same face of the m olecule. They include Asp64, Asp116, Glu152 and Lys159 from the core and Ar g231, Leu234, Arg262, Arg263 and Lys264 from the C-terminal domain. A model for DNA binding is proposed to bridge the two domains by tethering the 228 -236 loop of the C-terminal domain and the flexible loop of the core. (C) 2 000 Academic Press.