Dear Editor,
DEAD-box proteins, which are named after the strictly conserved amino acid sequence
Asp-Glu-Ala-Asp, were first identified as a distinct family in the late 1980s when
alignments based on eight homologues of the yeast eIF4A highlighted the presence of
several conserved motifs (Linder et al., 1989). DEAD-box proteins are widely distributed
in different life forms, ranging from bacteria to human and constitute the largest
RNA helicase family (Jiang et al., 2016). They are involved in many aspects of RNA
metabolism, such as splicing, mRNA export, transcriptional and translational regulation,
ribosome biogenesis and RNA decay (Rocak and Linder, 2004). The core of DEAD-box proteins
is organized into two major domains. Domain 1 (DEAD domain) consists of motifs Q,
I (Walker A, P-loop), II (Walker B, DEAD-box), Ia, GG, Ib and III, whereas domain
2 (Helicase domain) consists of motifs IV, V and VI. Different motifs are involved
in nucleotide binding (Q, I and II), RNA binding (Ia, Ib, IV and V) and ATP hydrolysis
(III and possibly VI). Compared with the two conserved domains, the N- and C-terminal
regions are variable and divergent. Their functions are not fully characterized, but
they are thought to confer their own specificity on different proteins (Hogbom et
al., 2007).
The recognition of pathogen-associated molecular patterns (PAMPs) of pathogens by
pattern recognition receptors (PRRs) is important for the induction of type I interferons
(IFN) (Medzhitov and Janeway, 2000). DDX41, a member of the DEAD-box proteins, containing
a disordered N-terminal region, a DEAD domain and a Helicase domain (Fig. 1A), was
identified as an intracellular DNA sensor in myeloid dendritic cells (mDCs) by Yong-Jun
Liu’s group. They showed that DDX41 directly binds DNA and STING via its DEAD domain
and triggers activation of signaling mediated by mitogen-activated protein kinases
TBK1 and transcription factor IRF3, resulting IFN production (Zhang et al., 2011).
DDX41 can also detect bacterial secondary messengers like cyclic di-GMP (c-di-GMP)
and cyclic di-AMP (c-di-AMP), leading to formation of a complex with STING. This complex
transmits the signal of bacterial intrusion to TBK1-IRF3 and activates the interferon
response (Parvatiyar et al., 2012). Phosphorylation of Tyr414 of DDX41 is a pre-requisite
for foreign dsDNA recognition and recruitment of STING. Besides, BTK’s kinase domain
can bind the DEAD domain of DDX41 (Lee et al., 2015). After immune response, DDX41
will be ubiquitinated by TRIM21 through K48-mediated linkage for degradation. The
ubiquitination sites are Lys9 and Lys115 (Zhang et al., 2013). Somatic DDX41 mutations
have been reported in the study of sporadic acute myeloid leukemia (AML) syndrome
(Ding et al., 2012). A familial MDS/AML syndrome characterized by long latency and
germline mutations in DDX41 gene is also identified (Polprasert et al., 2015). DDX41
can associate with spliceosomal proteins, and its defects lead to loss of tumor suppressor
function due to altered pre-mRNA splicing and RNA processing (Polprasert et al., 2015).
Although DDX41 plays important roles in innate immunity and diseases, the precise
mechanism as well as the extent of involvement the protein in these processes is poorly
understood.
Figure 1
Overall structure of hDDX41 DEAD domain. (A) Domain organization of hDDX41, composing
of DEAD domain and Helicase domain from N to C terminus. (B) A ribbon representation
of DEAD domain with secondary structural elements labeled. Helix, sheet and loop are
colored in red, yellow and green, respectively. (C) The multiangle static light scattering
result of DEAD domain protein. The calculated molecular weight is 29.3 kDa. (D) Structure
alignment of hDDX41 (wheat) to the structure of DDX5 (light blue) in complex with
ADP (in white sticks from PDB code: 3FE2) reveals that the bound SO4
2− (yellow sticks) is located in approximately the same position of α-phosphate of
ADP. The bound SO4
2− of hDDX41 and ADP are shown sticks. (E) The SO4
2− is coordinated by P-loop and the Mg2+ is coordinated by T227, K231 from P-loop
and E345 from motif II. The electron density map (2Fo-Fc) of SO4
2−, Mg2+, T227, K231 and E345 is contoured at 1.0 σ. (F) Superposition of the P-loop
of hDDX41 with SO4
2− (wheat), Prp28 (yellow), DDX3X with AMP (red), DDX5 with ADP (cyan), VASA with
ANP (green)
Here, we report the crystal structure of human DDX41 (hDDX41) DEAD domain complexed
with an SO4
2− and an Mg2+ to 2.26 Å resolution. There are strong interactions between different
motifs to stabilize the whole structure. The P-loop presents in a half-open conformation.
The DEAD domain protein can bind ADP and AMP but not ATP in vitro because of the steric
hindrance. Most mutated amino acids related with familial MDS/AML are conserved. In
addition, the N-terminal disordered region (amino acid 1–152) is shown targeting hDDX41
protein to the nucleus. Our study provides basic structural information for further
researches on hDDX41 biological function and valuable insights for the treatment of
DDX41-related diseases in the future.
The crystal structure of hDDX41 DEAD domain was solved by molecular replacement using
the structure of DDX5 domain I (PDB code: 3FE2) as the search model and refined to
2.26 Å resolution with an R factor of 0.19 (Rfree = 0.23). Details of data collection
and refinement statistics are listed in Table S1. The crystal used for data collection
belonged to space group P21. One asymmetric unit consists of two molecules of the
protein based on the calculated solvent content of 44.15%. The hDDX41 DEAD domain
consists of an α/β fold, which is similar to those observed for other members of the
DEAD-box proteins for which structures are available. The overall structure consists
of ten α-helices (α1–α10) and a β-sheet formed by eight β-strands (β1–β8). Helices
α1–α5 are located on one side of the β-sheet, while helices α6–α10 are located on
the other side (Fig. 1B). Although there are two monomers in one asymmetric unit,
PDBePISA (http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver) predicted a monomeric
biological assembly. In agreement with this prediction, results of the static light
scattering analysis indicated that the DEAD domain exists as a monomer in solution
(Fig. 1C).
Although ADP or AMP was added in molar excess to the protein prep before crystallization,
no electron density was observed for these ligands. Instead, clear electron density
for one SO4
2− probably originating from the crystallization solution, was observed in the nucleotide-binding
site. When aligned to the structure of DDX5 in complex with ADP (PDB code: 3FE2),
the SO4
2− overlaps with the position of α-phosphate of ADP (Fig. 1D). The P-loop is seen
forming the SO4
2− binding pocket and an Mg2+ is observed coordinated by T227, K231 from P-loop and
E345 from motif II (Fig. 1E). Mutating P-loop or motif II to alanine resulted in insoluble
protein. The structure of DDX41 DEAD domain solved by us contains motif Q, P-loop,
motif II, motif Ia, motif Ib and motif III. These structural elements are located
at either β-strand-loop or helix-loop transitions (Fig. S1). There are many interactions
between the different motifs, which probably stabilizes the overall structure. These
interactions are listed in Table S2.
The P-loop is responsible for the nucleotide binding. Fig. 1F shows superposition
of the P-loop of hDDX41 with SO4
2− (wheat), Prp28 (yellow, PDB code 4NHO), DDX3X with AMP (red, PDB code 2I4I), DDX5
with ADP (cyan, PDB code 3FE2), VASA with ANP (green, PDB code 2DB3). It seems that
the P-loop is not restricted to one open or closed conformation but has a flexibility
that allows it to adapt to different conformations depending on the binding ligands.
The most closed conformation is found in Prp28, which leaves no room for any ligand.
The most open conformation is found in VASA, which has enough space for ANP. The P-loop
of DDX3X with AMP and DDX5 with ADP adopt the same half-open conformation compared
with Prp28 and VASA. Although there is no nucleotide in the solved hDDX41 structure,
the SO4
2− bound P-loop adopts a half-open conformation. The P-loop has a shift in Cα-atom
positions by up to 2.7 Å between the open and half-open states, and by up to 1.7 Å
between the half-open and closed states (Fig. 1F). The conformation of the P-loop
seems to be determined by the nucleotide phosphates, and longer phosphate tails result
in a more open loop. During our manuscript submission, Omura et al. reported two similar
crystal structures of the DDX41 DEAD domain with root-mean-square deviation (RMSD)
of 0.5 Å between the main chain Cα atoms of the 330 amino acids (Fig. S2) (Omura et
al., 2016).
The binding affinity of hDDX41 DEAD domain with ATP, ADP, AMP, c-di-GMP and cGAMP
was detected in vitro by Thermal Shift Assay (TSA) and Isothermal Titration Calorimetry
(ITC) (Fig. 2A). The thermal denaturation profiles indicated a Tm of 41°C for unliganded
hDDX41 DEAD domain. Addition of ATP, c-di-GMP, and cGAMP to the protein did not increase
the Tm. However, the Tm increased in presence of ADP and AMP by 2.2°C and 3.9°C, respectively,
implying that the protein probably binds ADP and AMP but not ATP. There was no detectable
interaction between hDDX41 DEAD domain with c-di-GMP and cGAMP, although the full
length protein is reported to bind c-di-GMP (Parvatiyar et al., 2012). ITC results
suggested a binding affinity of 31 µM and 61 µM for ADP and AMP, respectively. Furthermore,
the ITC results indicated that the DEAD domain of DDX41 does not interact with ATP,
c-di-GMP, or cGAMP, which is consistent with the TSA results. AMP or ADP could be
modeled into the binding pocket of hDDX41 DEAD domain by superimposing the crystal
structure of VASA (PDB code: 2DB3) and DDX5 (PDB code: 3FE2) over that of DDX41. The
adenosine moiety fits well into the pocket and the α-, β-phosphate can also be accommodated.
However, a γ-phosphate as in the case of ATP would clash with T227 of the P-loop (Fig. 2B).
The negatively charged binding pocket is not big enough for ATP (Fig. 2B). This may
explain why we could not detect any significant affinity of the protein for ATP in
vitro.
Figure 2
The binding of hDDX41 DEAD domain with different molecules and N-terminal region targets
hDDX41 to the nucleus. (A) Thermal Shift Assay and Isothermal Titration Calorimetry
of hDDX41 DEAD domain protein with ATP, ADP, AMP, c-di-GMP and cGAMP. (B) Left: the
modeled ADP and ANP are colored in cyan and green. The γ-phosphate of ANP clashes
with T227 of hDDX41. Right: surface electrostatic potential representation of the
nucleotide binding pocket. Blue, positive potential; red, negative potential. The
positively charged binding pocket is not big enough for ANP binding. (C) Fluorescence
microscopy of HEK293T cells transfected with expression plasmids for GFP-tagged hDDX41
full length protein (1–622) and GFP-tagged hDDX41 N-terminal region deleted truncation
(153–622). Nuclei are stained with DAPI
hDDX41 is frequently mutated in familial MDS/AML (Polprasert et al., 2015). We analyzed
the conservation of hDDX41 amino acids using the ConSurf Server (http://consurf.tau.ac.il/)
and found out that the mutated amino acids associated with MDS/AML are conserved (Fig.
S3). Of the nine mutations identified, seven mutations (p.M155I, p.R164W, p.F183I,
p.A225D, p.E247K, p.P321L, p.I396T) are locate in the DEAD domain, suggesting hDDX41
function is more sensitive to mutations in DEAD domain than Helicase domain. MDS/AML
is now the only reported disease related to hDDX41 protein. However, the relationship
between the mutations and disease is still unknown. hDDX41 could serve as a drug target
and our study provides a structural basis for disease treatment.
Secondary structure prediction of hDDX41 (Fig. S4) reveals that the N-terminal region
(aa 1–160) is disordered. In addition, the role of this region is unclear. Interestingly,
the N-terminal 1–194 amino acids of a homologue of DDX41, Abstrkt, from Drosophila
play a role in the translocation of the protein to the nucleus (Abdul-Ghani et al.,
2005). Alignment of the N-terminal regions of the two proteins shows that they share
41.9% identity (Fig. S5). We generated GFP-fusions of full length hDDX41 and truncations
of hDDX41 missing aa 153–622 and monitored their cellular localization after transfection
in HEK293T cells. GFP-fusions containing the full length protein showed nuclear localization
while deletion of aa 153–622 resulted in distinct punctate cytoplasmic distribution
and loss of nuclear localization (Fig. 2C). Taken together, we conclude that the N-terminal
disordered region (aa 1–152) of hDDX41 can target the protein to the nucleus.
DDX41 is reported to bind dsDNA and c-di-GMP directy by DEAD domain. However, the
affinity of DEAD domain with dsDNA and c-di-GMP can’t be detected in vitro. Different
lengths of dsDNA and c-di-GMP were tested by TSA, ITC and Surface Plasmon Resonance
(SPR) assay, but no binding was detected. As intracellular condition is much more
complicated, DDX41’s functions in innate immunity may need other components or depends
on both domains. Besides c-di-GMP, STING is also a direct sensor of c-di-GMP (Burdette
et al., 2011). We solved the complex structure of hSTING (aa 139–379) and c-di-GMP
(Ouyang et al., 2012). One c-di-GMP binds to the interface of STING dimer with a unique
mode. We mixed c-di-GMP with hDDX41 DEAD domain before crystallization, but there
is no electron density for c-di-GMP in the structure.
In summary, we report the crystal structure of hDDX41 DEAD domain complexed with an
SO4
2− and an Mg2+ to 2.26 Å resolution. But the mechanism of hDDX41 recognition with
foreign dsDNA and c-di-GMP remains unclear. Our study provides basic structural information
for further researches on DDX41 biological functions and the treatment of DDX41-related
diseases in the future.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Supplementary material 1 (PDF 500 kb)