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.

Keywords: DEAH-box; DEAH/RHA family; DHX15; RNA helicase 15; innate immunity.

Figure 1

Sequence alignment between DHX15 and Prp43. A sequence alignment of DHX15 from human (DHX15_HUMAN), mouse (DHX15_MOUSE) and Drosophila melanogaster (DHX15_DROME) and of Prp43 from Saccharomyces cerevisiae (PRP43_YEAST) and Chaetomium thermophilum (PRP43_CHATD) is shown. The sequences were derived from UniProt (http://www.uniprot.org/) and were aligned using CLUSTALW (http://www.genome.jp/tools/clustalw/). The figure was prepared using ESPript3 (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi; Robert & Gouet, 2014 ▸). The secondary structure of human DHX15 is shown at the top of each block. The residues involved in the interaction with ssRNA in ctPrp43 (Tauchert et al., 2017 ▸) are highlighted with black stars.

Figure 2

Overall structure of the ADP-bound form of DHX15. The ADP molecule is recognized by two RecA domains with a typical arrangement that is conserved in the helicase family. The front view (left) and side view (right) are shown. Each domain is coloured: the N-terminal extension in brown, the RecA1 domain in light green, the RecA2 domain in magenta, the WH domain in red, the ratchet domain in violet and the OB-fold domain in orange. The double-headed arrow at the bottom indicates the region contained in the final model.

Figure 3

Structures of sequence motifs of DHX15 conserved in the helicase family. (a) Motifs Ia, Ib, III and IV, which are involved in binding to and unwinding of nucleic acid ligands. (b) Motifs I, II, V and VI, which are involved in nucleotide recognition. (c) ADP recognition by DHX15. The motifs are coloured in black in (a) and (b). Motifs I–III are located in the RecA1 domain and motifs IV–VI in the RecA2 domain. Polar interactions are indicated by dashed black lines. A magnesium ion and water molecules, which mediate ADP recognition, are shown as a grey sphere and red spheres, respectively.

Figure 4

Electrostatic surface potential of DHX15. (a) The molecular surface of DHX15, showing electrostatic surface potential, viewed from the RecA2 and CTD sides. (b) Cutaway surface showing the inner surface of the pocket, viewed from the CTD side. The electrostatic surface potential, calculated using APBS (Baker et al., 2001 ▸), was visualized with CueMol (http://www.cuemol.org). Positively charged and negatively charged surfaces are coloured blue and red, respectively. Some residues are labelled.

Figure 5

Structural comparison between DHX15 and Prp43. (a) Cartoon models of the ADP-bound forms of human DHX15 (hDHX15; this study), scPrp43 (PDB entry 2xau; Walbott et al., 2010 ▸) and ctPRP43 (PDB entry 5d0u; Tauchert et al., 2016 ▸). (b) Superposition of these three structures coloured as follows: hDHX15, violet–pink; scPrp43, blue; ctPrp43, cyan. (c) ADP recognition by hDHX15 (left), scPrp43 (middle) and ctPrp43 (right). (d) The structures of the OB-fold domains of hDHX15 (violet–pink), scPrp43 (blue) and ctPrp43 (cyan). The residues of scPrp43 that are involved in the interactions with Ntr1 (Christian et al., 2014 ▸) and with RNA (Walbott et al., 2010 ▸) are coloured yellow and green, respectively. The residues that are implicated in interaction with RNA and the G-patch domain-containing protein Ntr1 in scPrp43 are mostly conserved in hDHX15.