title: Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.
abstract: How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the 'closed-state' helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.
authors.affiliation: Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States.
authors.forename: Anna L
authors.initials: AL
authors.lastname: Mallam
authors.affiliation: Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States.
authors.forename: David J
authors.initials: DJ
authors.lastname: Sidote
authors.affiliation: Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States.
authors.forename: Alan M
authors.initials: AM
authors.lastname: Lambowitz
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D053487:DEAD-box RNA Helicases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004271:DNA, Fungal / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D015870:Gene Expression; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012331:RNA, Fungal / Q000737:chemistry* / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D013379:Substrate Specificity
chemical_list: D004271:DNA, Fungal; D009841:Oligonucleotides; D012331:RNA, Fungal; D011994:Recombinant Proteins; D029701:Saccharomyces cerevisiae Proteins; C058150:MSS116 protein, S cerevisiae; D053487:DEAD-box RNA Helicases
keywords: DEAD-box protein; RNA helicase; RNA unwinding; S. cerevisiae; biochemistry; biophysics; enzyme mechanism; enzyme specificity; molecular evolution; structural biology