title: Alternative native flap conformation revealed by 2.3 A resolution structure of SIV proteinase.
abstract: A large conformational change is observed between HIV-1 proteinase in the ligand-free state and in complexes with transition-state inhibitors. Crystal structures of this enzyme have either the flaps open for the native or ligand-free enzyme or the flaps closed for peptidomimetic ligand-bound enzyme. We describe the structure of native recombinant SIV proteinase which like other retroviral proteinases crystallizes as a perfect 2-fold symmetric dimer but in a different crystal packing arrangement. In contrast to HIV-1 PR we show that SIV proteinase in the ligand-free state adopts the closed flaps conformation, demonstrating that ligand binding is not a prerequisite for the closed flaps conformation. The catalytic water was clearly observed between the two aspartates which were not perfectly co-planar, and in this structure the active site cleft is more restricted than for either inhibitor bound or ligand-free HIV-1 proteinase. Accommodation of two bulkier side-chains in the simian enzyme core has resulted in a more exposed N terminus than for HIV-1 PR which we predict could enhance autocatalytic cleavage at the N terminus.
authors.affiliation: Department of Crystallography, Birkbeck College, London, England.
authors.forename: A F
authors.initials: AF
authors.lastname: Wilderspin
authors.forename: R J
authors.initials: RJ
authors.lastname: Sugrue
mesh_terms: D000595:Amino Acid Sequence; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry* / Q000235:genetics; D001665:Binding Sites; D016333:HIV Protease / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011487:Protein Conformation; D016415:Sequence Alignment; D015302:Simian Immunodeficiency Virus / Q000201:enzymology*
chemical_list: D016282:Aspartic Acid Endopeptidases; D016333:HIV Protease; C077164:SIV(mac) proteinase