The crystal structure of human DEAH-box RNA helicase 15 reveals a domain organization of the mammalian DEAH/RHA family

Abstract

DEAH-box RNA helicase 15 (DHX15) plays important roles in RNA metabolism, including in splicing and in ribosome biogenesis. In addition, mammalian DHX15 also mediates the innate immune sensing of viral RNA. However, structural information on this protein is not available, although the structure of the fungal orthologue of this protein, Prp43, has been elucidated. Here, the crystal structure of the ADP-bound form of human DHX15 is reported at a resolution of 2.0 Å. This is the first structure to be revealed of a member of the mammalian DEAH-box RNA helicase (DEAH/RHA) family in a nearly complete form, including the catalytic core consisting of the two N-terminal RecA domains and the C-terminal regulatory domains (CTD). The ADP-bound form of DHX15 displayed a compact structure, in which the RecA domains made extensive contacts with the CTD. Notably, a potential RNA-binding site was found on the surface of a RecA domain with positive electrostatic potential. Almost all structural features were conserved between the fungal Prp43 and the human DHX15, suggesting that they share a fundamentally common mechanism of action and providing a better understanding of the specific mammalian functions of DHX15.

Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases

“…Further research is needed to gain better understanding of the activities of DHX15. As of May 2017, DHX15 is the only DEAH-box helicase whose crystal structure has been revealed in a nearly-complete form, lacking only the N-terminal extension domain [156]. DHX15 is divided into six structural domains, namely the N-terminal extension, the RecA1 and RecA2 domains, the winged-helix domain, the ratchet domain and the oligonucleotide /oligosaccharidebinding (OB)-fold domain.…”

“…DHX15 is divided into six structural domains, namely the N-terminal extension, the RecA1 and RecA2 domains, the winged-helix domain, the ratchet domain and the oligonucleotide /oligosaccharidebinding (OB)-fold domain. Among them, the OB-fold domain is important for interaction with the G-patch proteins, such as NKRF [100,156].…”

“…The putative RNA binding pocket is located between the two RecA domains and the C-terminal domain (containing the winged-helix domain, the ratchet domain and the OB-fold domain) [156]. Based on the mechanism by which Prp43 (the fungal orthologue of DHX15) binds ssRNA, the 153 ROLES OF DEAD/DEAH-BOX HELICASES authors suggest that binding of ATP and RNA triggers a structural rearrangement in the RNA binding pocket to form an RNA-accommodating groove [156]. However, DHX15 senses viral RNA in an ATPase-independent manner, indicating existence of other factors that cause the structural rearrangement of the RNA binding pocket.…”

“…Similarly to DDX41, DHX15 has also been implied in the pathogenesis of acute myeloid leukemia (AML) [157]. The mutation of the highly conserved arginine significant for RNA binding (R222G) is related to AML, and the overexpression of DHX15 in the AML patients indicates poor cytogenic prognosis and overall survival [156,157]. Of note, overexpressed DHX15 in AML acts through activation of NF-κB pathway just as during the viral infection, but it decreases the levels of caspase-3 and PARP, thereby promoting cell survival [157].…”

Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs

“…Unlike DEAD-box proteins, which contain a wide variety of non-conserved C-terminal extensions, DEAH-box proteins share a highly-conserved C-terminus made up of three domains: a winged helix (WH), a ratchet-like domain, and an oligosaccharide binding (OB) fold (45). Crystal structure show that these C-terminal domains interact strongly with the helicase core, yielding an enzyme with less flexibility in the core than DEAD-box proteins (47–49). …”