spacer Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases
Primary citation
Title Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases.
Authors Zhao, K.search; Harshaw, R.search; Chai, X.search; Marmorstein, R.search
Journal PROC.NATL.ACAD.SCI.USAsearch vol:101, pag:8563-8568 (2004), Identifiers: PubMed ID (15150415)search DOI (10.1073/pnas.0401057101)
Abstract Sir2 enzymes are broadly conserved from bacteria to humans and have been implicated to play roles in gene silencing, DNA repair, genome stability, longevity, metabolism, and cell physiology. These enzymes bind NAD(+) and acetyllysine within protein targets and generate lysine, 2'-O-acetyl-ADP-ribose, and nicotinamide products. To provide structural insights into the chemistry catalyzed by Sir2 proteins we report the high-resolution ternary structure of yeast Hst2 (homologue of Sir two 2) with an acetyllysine histone H4 peptide and a nonhydrolyzable NAD(+) analogue, carba-NAD(+), as well as an analogous ternary complex with a reaction intermediate analog formed immediately after nicotinamide hydrolysis, ADP-ribose. The ternary complex with carba-NAD(+) reveals that the nicotinamide group makes stabilizing interactions within a binding pocket harboring conserved Sir2 residues. Moreover, an asparagine residue, N116, strictly conserved within Sir2 proteins and shown to be essential for nicotinamide exchange, is in position to stabilize the oxocarbenium intermediate that has been proposed to proceed the hydrolysis of nicotinamide. A comparison of this structure with the ADP-ribose ternary complex and a previously reported ternary complex with the 2'-O-acetyl-ADP-ribose reaction product reveals that the ribose ring of the cofactor and the highly conserved beta1-alpha2 loop of the protein undergo significant structural rearrangements to facilitate the ordered NAD(+) reactions of nicotinamide cleavage and ADP-ribose transfer to acetate. Together, these studies provide insights into the chemistry of NAD(+) cleavage and acetylation by Sir2 proteins and have implications for the design of Sir2-specific regulatory molecules.
MeSH terms Adenosine Diphosphate Ribosesearch, Binding Sitessearch, Histone Deacetylasessearch, Modelssearch, Molecularsearch, NADsearch, Niacinamidesearch, Protein Conformationsearch, Saccharomyces cerevisiaesearch, Silent Information Regulator Proteinssearch, Saccharomyces cerevisiaesearch, Sirtuin 2search, Sirtuinssearch, Thermodynamicssearch
Other entries described in this publication 1szc
Secondary citations
Title Structure and Autoregulation Of The Yeast Hst2 Homolog Of Sir2
Authors Zhao, K.search; Harshaw, R.search; Chai, X.search; Marmorstein, R.search
Journal NAT.STRUCT.MOL.BIOL.search vol:10, pag:864-871 (2003), Identifiers: PubMed ID (14502267)search DOI (10.1038/nsb978)
Abstract Yeast Hst2 (yHst2) is a member of the silencing information regulator 2 (Sir2) family of NAD(+)-dependent protein deacetylases that are implicated in transcriptional silencing, DNA repair, genome stability and longevity. The X-ray crystal structure of the full-length yHst2 protein reveals a central catalytic core domain fold that is characteristic of the other Sir2 homologs, and C- and N-terminal extensions that interact with the NAD(+) and acetyl-lysine substrate-binding sites, respectively, suggesting an autoregulatory function for these domains. Moreover, the N-terminal extension mediates formation of a homotrimer within the crystal lattice. Enzymatic and sedimentation equilibrium studies using deletion constructs of yHst2 support the involvement of the N- and C-terminal yHst2 regions and trimer formation in catalysis by yHst2. Together, these studies indicate that the sequence-divergent N- and C-terminal regions of the eukaryotic Sir2 proteins may have a particularly important role in their distinct substrate-binding properties, biological activities or both.
MeSH terms Amino Acid Sequencesearch, Binding Sitessearch, Crystallographysearch, X-Raysearch, Kineticssearch, Molecular Sequence Datasearch, NADsearch, Protein Bindingsearch, Protein Structuresearch, Tertiarysearch, Saccharomyces cerevisiaesearch, Saccharomyces cerevisiae Proteinssearch, Sirtuin 2search, Sirtuinssearch
Title Structure Of The Yeast Hst2 Protein Deacetylase In Ternary Complex With 2'-O-Acetyl ADP Ribose and Histone Peptide
Authors Zhao, K.search; Chai, X.search; Clements, A.search; Marmorstein, R.search
Journal STRUCTUREsearch vol:11, pag:1403-1411 (2003), Identifiers: PubMed ID (14604530)search DOI (10.1016/j.str.2003.09.016)
Abstract Sir2 proteins are NAD(+)-dependant protein deactylases that have been implicated in playing roles in gene silencing, DNA repair, genome stability, longevity, metabolism, and cell physiology. To define the mechanism of Sir2 activity, we report the 1.5 A crystal structure of the yeast Hst2 (yHst2) Sir2 protein in ternary complex with 2'-O-acetyl ADP ribose and an acetylated histone H4 peptide. The structure captures both ligands meeting within an enclosed tunnel between the small and large domains of the catalytic protein core and permits the assignment of a detailed catalytic mechanism for the Sir2 proteins that is consistent with solution and enzymatic studies. Comparison of the ternary complex with the yHst2/NAD(+) complex, also reported here, and nascent yHst2 structure also reveals that NAD(+) binding accompanies intramolecular loop rearrangement for more stable NAD(+) and acetyl-lysine binding, and that acetyl-lysine peptide binding induces a trimer-monomer protein transition involving nonconserved Sir2 residues.
MeSH terms Amino Acid Sequencesearch, Binding Sitessearch, Catalysissearch, Catalytic Domainsearch, Crystallographysearch, X-Raysearch, DNA Repairsearch, Histonessearch, Lysinesearch, Modelssearch, Chemicalsearch, Modelssearch, Molecularsearch, Molecular Sequence Datasearch, Peptidessearch, Protein Bindingsearch, Protein Conformationsearch, Protein Structuresearch, Tertiarysearch, Saccharomyces cerevisiaesearch, Saccharomyces cerevisiae Proteinssearch, Sirtuin 2search, Sirtuinssearch, Substrate Specificitysearch
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