title: Transition State Features in the Hepatitis Delta Virus Ribozyme Reaction Revealed by Atomic Perturbations.
abstract: Endonucleolytic ribozymes constitute a class of non-coding RNAs that catalyze single-strand RNA scission. With crystal structures available for all of the known ribozymes, a major challenge involves relating functional data to the physically observed RNA architecture. In the case of the hepatitis delta virus (HDV) ribozyme, there are three high-resolution crystal structures, the product state of the reaction and two precursor variants, with distinct mechanistic implications. Here, we develop new strategies to probe the structure and catalytic mechanism of a ribozyme. First, we use double-mutant cycles to distinguish differences in functional group proximity implicated by the crystal structures. Second, we use a corrected form of the Brønsted equation to assess the functional significance of general acid catalysis in the system. Our results delineate the functional relevance of atomic interactions inferred from structure, and suggest that the HDV ribozyme transition state resembles the cleavage product in the degree of proton transfer to the leaving group.
authors.forename: Selene C
authors.initials: SC
authors.lastname: Koo
authors.forename: Jun
authors.initials: J
authors.lastname: Lu
authors.forename: Nan-Sheng
authors.initials: NS
authors.lastname: Li
authors.forename: Edward
authors.initials: E
authors.lastname: Leung
authors.affiliation: ‡Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.
authors.forename: Subha R
authors.initials: SR
authors.lastname: Das
authors.affiliation: §Department of Biochemistry and Center for Proteomics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Harris
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Piccirilli
mesh_terms: D001483:Base Sequence; D020134:Catalytic Domain; D003699:Hepatitis D / Q000821:virology*; D003698:Hepatitis Delta Virus / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011522:Protons; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*
chemical_list: D011522:Protons; D016337:RNA, Catalytic; D012367:RNA, Viral