{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["389(Pt 2)"],"submitter":["Kumar M"],"pubmed_abstract":["HIV-1 protease is an effective target for the design of drugs against AIDS. To help this process of drug design, three-dimensional structures have been determined of complexes between HIV-1 protease and a variety of transition-state analogue inhibitors. The true transition state, however, has not been structurally characterized. The crystal structure of the C95M/C1095A HIV-1 protease tethered dimer shows a distinctive feature in which the two flaps of the enzyme are in a 'closed conformation' even in the unliganded state. This unique feature has been utilized here to study the structure of HIV-1 protease complexed to an oligopeptide substrate of amino acid sequence His-Lys-Ala-Arg-Val-Leu*NPhe-Glu-Ala-Nle-Ser (where * denotes the cleavage site, and NPhe and Nle denote p-nitrophenylalanine and norleucine residues respectively). The X-ray structure of the complex refined against 2.03 A (0.203 nm) resolution synchrotron data shows that the substrate is trapped as a tetrahedral reaction intermediate in the crystal. The hydrogen-bonding interactions between the reaction intermediate and the catalytic aspartates are different from those observed previously using transition-state analogues. The reaction intermediate did not dissociate to release the products, possibly due to the inflexibility introduced in the flaps when the enzyme is packed inside crystals."],"journal":["The Biochemical journal"],"pagination":["365-71"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC1175113"],"repository":["biostudies-literature"],"pubmed_title":["Observation of a tetrahedral reaction intermediate in the HIV-1 protease-substrate complex."],"pmcid":["PMC1175113"],"pubmed_authors":["Mahale S","Prashar V","Kumar M","Hosur MV"],"additional_accession":[]},"is_claimable":false,"name":"Observation of a tetrahedral reaction intermediate in the HIV-1 protease-substrate complex.","description":"HIV-1 protease is an effective target for the design of drugs against AIDS. To help this process of drug design, three-dimensional structures have been determined of complexes between HIV-1 protease and a variety of transition-state analogue inhibitors. The true transition state, however, has not been structurally characterized. The crystal structure of the C95M/C1095A HIV-1 protease tethered dimer shows a distinctive feature in which the two flaps of the enzyme are in a 'closed conformation' even in the unliganded state. This unique feature has been utilized here to study the structure of HIV-1 protease complexed to an oligopeptide substrate of amino acid sequence His-Lys-Ala-Arg-Val-Leu*NPhe-Glu-Ala-Nle-Ser (where * denotes the cleavage site, and NPhe and Nle denote p-nitrophenylalanine and norleucine residues respectively). The X-ray structure of the complex refined against 2.03 A (0.203 nm) resolution synchrotron data shows that the substrate is trapped as a tetrahedral reaction intermediate in the crystal. The hydrogen-bonding interactions between the reaction intermediate and the catalytic aspartates are different from those observed previously using transition-state analogues. The reaction intermediate did not dissociate to release the products, possibly due to the inflexibility introduced in the flaps when the enzyme is packed inside crystals.","dates":{"release":"2005-01-01T00:00:00Z","publication":"2005 Jul","modification":"2025-05-18T10:59:57.874Z","creation":"2025-05-18T10:59:57.874Z"},"accession":"S-EPMC1175113","cross_references":{"pubmed":["15794743"],"doi":["10.1042/bj20041804","10.1042/BJ20041804"]}}