Structural studies of viperin, an antiviral radical SAM enzyme

Abstract

Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SAH) or 5′-deoxyadenosine (5′-dAdo) and L-methionine (L-Met). Viperin contains a partial (βα) 6 -barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first β-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5′-dAdo and L-Met (SAM cleavage products) is consistent with the canonical mechanism of 5′-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. The viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTPbinding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.radical SAM | IFN-stimulated gene | antiviral cellular factor | free radical | S-adenosyl methionine V iruses exploit the metabolic machinery of host cells to replicate and spread to other cells. Although cytotoxic T cells and antibody-producing B cells can ultimately be produced in an adaptive response to the virus, innate immune mechanisms are used to respond to infection rapidly. Upon infection, cells can sense the presence of virus via pattern recognition receptors (1, 2) and produce IFNs that limit the spread of infection to other cells (3). IFNs induce the expression of hundreds of IFN-stimulated genes (ISGs), many of which are involved in various antiviral processes, including antigen presentation, apoptosis, and inhibition of viral replication (4-7).Viperin, the product of rsad-2, was first identified as a protein induced by exposure of human macrophages to IFN-γ and by infection of primary human fibroblasts with human cytomegalovirus (8,9). Early studies showed that viperin is induced in various cell types by IFN-α and IFN-β, associates with the cytosolic face of the endoplasmic reticulum (ER), and inhibits human cytomegalovirus replication when preexpressed in human fibroblasts (8). Since then, viperin has been shown to be induced by several factors, including lipopolysaccharide (10-12), and to inhibit a broad range of viruses, including HIV-1 (13), West Nile virus (14), hepatitis C virus (15, 16), dengue virus type 2 (17), influ...

Human viperin catalyzes the modification of GPP and FPP potentially affecting cholesterol synthesis

“…The mouse construct was expressed by the addition of 0.2 mM IPTG as described in reference [26]. For the human, falcon and chinchilla constructs, 2 L of LB medium was inoculated with 20 mL of precultured Escherichia coli BL21-DE3-CodonPlus (RIL) cells containing the construct of interest until an O.D.…”

“…The last purification step of the mouse viperin involved changing the buffer solution used in the HiTrap Desalting column (GE Healthcare TM ) to a 25 mM NaCl, 5 mM HEPES buffer, pH 7.1 as described [26]. The reconstitution of the iron-sulfur cluster was performed by the addition of 5 mM DTT, 1 mM FeCl 3 and 1 mM Na 2 S to the crude extract under mild stirring for 2 h at 18°C.…”

“…5). This patch composed of conserved lysine and arginine residues, which in the mouse viperin correspond to K120 (K119 in human), R245 (R244), K220 (K219), and K247 (K246) is strictly conserved in all known viperin sequences and has been proposed to be involved in substrate binding [26]. This patch composed of conserved lysine and arginine residues, which in the mouse viperin correspond to K120 (K119 in human), R245 (R244), K220 (K219), and K247 (K246) is strictly conserved in all known viperin sequences and has been proposed to be involved in substrate binding [26].…”

“…Analysis of this structure shows that a patch of basic residues is located at the bottom of the ¾ b-barrel. Fenwick et al [26] also outlined the high similarity between viperin and MoaA, another radical SAM enzyme that uses guanosine triphosphate as substrate Fig. Fenwick et al [26] also outlined the high similarity between viperin and MoaA, another radical SAM enzyme that uses guanosine triphosphate as substrate Fig.…”

“…2) [7]. The recently published structure of the mouse viperin suggests instead that a nucleotide triphosphate could be its substrate [26]. Furthermore, recent biochemical studies have not found any modification of the viperin activity in the presence of FPPS.…”