Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p

• Published in: Nature (London) 2012-10, Vol.490 (7418), p.121-125
• Main Authors: Mallam, Anna L., Del Campo, Mark, Gilman, Benjamin, Sidote, David J., Lambowitz, Alan M.
• Format: Article
• Language: English
• Subjects: 631/337/1645; 631/45/535; 631/45/607/275; Adenosine Triphosphatases - chemistry; Adenosine Triphosphatases - metabolism; Adenosine Triphosphate - metabolism; Amino Acid Motifs; Analysis; ATP; Base Sequence; Catalytic Domain; Conserved Sequence; Crystal structure; Crystallography, X-Ray; DEAD-box RNA Helicases - chemistry; DEAD-box RNA Helicases - metabolism; Deoxyribonucleic acid; DNA; Enzymes; Evolution, Molecular; GC Rich Sequence - genetics; Genetic research; Helicases; Humanities and Social Sciences; letter; Mode of action; Models, Molecular; multidisciplinary; Nucleic Acid Conformation; Nucleic acids; Observations; Protein Structure, Tertiary; Proteins; RNA; RNA, Double-Stranded - chemistry; RNA, Double-Stranded - genetics; RNA, Double-Stranded - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - metabolism; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; Science; Science (multidisciplinary); Structure; Structure-Activity Relationship; Studies; Substrate Specificity; Yeasts
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature11402

Analysis of the yeast DEAD-box nucleic acid helicase Mss116p provides a structural model for how DEAD-box proteins recognize and unwind RNA duplexes. DEAD-box protein recognition of duplex RNA Alan Lambowitz and colleagues have solved the structure of Mss116, a yeast DEAD-box protein, bound to double-stranded RNA and a DNA–RNA hybrid. DEAD-box proteins are nucleic acid helicases that function to unwind and remodel RNAs and RNA-protein complexes. The structure shows the enzyme in a pre-unwound state, with ATP and RNA bound to different domains; it is proposed that a conformational change brings them together during unwinding. The structure also reveals how the enzyme discriminates between A-form RNA and B-form DNA. DEAD-box proteins are the largest family of nucleic acid helicases, and are crucial to RNA metabolism throughout all domains of life 1 , 2 . They contain a conserved ‘helicase core’ of two RecA-like domains (domains (D)1 and D2), which uses ATP to catalyse the unwinding of short RNA duplexes by non-processive, local strand separation 3 . This mode of action differs from that of translocating helicases and allows DEAD-box proteins to remodel large RNAs and RNA–protein complexes without globally disrupting RNA structure 4 . However, the structural basis for this distinctive mode of RNA unwinding remains unclear. Here, structural, biochemical and genetic analyses of the yeast DEAD-box protein Mss116p indicate that the helicase core domains have modular functions that enable a novel mechanism for RNA-duplex recognition and unwinding. By investigating D1 and D2 individually and together, we find that D1 acts as an ATP-binding domain and D2 functions as an RNA-duplex recognition domain. D2 contains a nucleic-acid-binding pocket that is formed by conserved DEAD-box protein sequence motifs and accommodates A-form but not B-form duplexes, providing a basis for RNA substrate specificity. Upon a conformational change in which the two core domains join to form a ‘closed state’ with an ATPase active site, conserved motifs in D1 promote the unwinding of duplex substrates bound to D2 by excluding one RNA strand and bending the other. Our results provide a comprehensive structural model for how DEAD-box proteins recognize and unwind RNA duplexes. This model explains key features of DEAD-box protein function and affords a new perspective on how the evolutionarily related cores of other RNA and DNA helicases diverged to use different mechanisms.