title: Zika Virus Methyltransferase: Structure and Functions for Drug Design Perspectives.
abstract: TheFlavivirusZika virus (ZIKV) is the causal agent of neurological disorders like microcephaly in newborns or Guillain-Barre syndrome. Its NS5 protein embeds a methyltransferase (MTase) domain involved in the formation of the viral mRNA cap. We investigated the structural and functional properties of the ZIKV MTase. We show that the ZIKV MTase can methylate RNA cap structures at the N-7 position of the cap, and at the 2'-O position on the ribose of the first nucleotide, yielding a cap-1 structure. In addition, the ZIKV MTase methylates the ribose 2'-O position of internal adenosines of RNA substrates. The crystal structure of the ZIKV MTase determined at a 2.01-Å resolution reveals a crystallographic homodimer. One chain is bound to the methyl donor (S-adenosyl-l-methionine [SAM]) and shows a high structural similarity to the dengue virus (DENV) MTase. The second chain lacks SAM and displays conformational changes in the αX α-helix contributing to the SAM and RNA binding. These conformational modifications reveal a possible molecular mechanism of the enzymatic turnover involving a conserved Ser/Arg motif. In the second chain, the SAM binding site accommodates a sulfate close to a glycerol that could serve as a basis for structure-based drug design. In addition, compounds known to inhibit the DENV MTase show similar inhibition potency on the ZIKV MTase. Altogether these results contribute to a better understanding of the ZIKV MTase, a central player in viral replication and host innate immune response, and lay the basis for the development of potential antiviral drugs.IMPORTANCEThe Zika virus (ZIKV) is associated with microcephaly in newborns, and other neurological disorders such as Guillain-Barre syndrome. It is urgent to develop antiviral strategies inhibiting the viral replication. The ZIKV NS5 embeds a methyltransferase involved in the viral mRNA capping process, which is essential for viral replication and control of virus detection by innate immune mechanisms. We demonstrate that the ZIKV methyltransferase methylates the mRNA cap and adenosines located in RNA sequences. The structure of ZIKV methyltransferase shows high structural similarities to the dengue virus methyltransferase, but conformational specificities highlight the role of a conserved Ser/Arg motif, which participates in RNA and SAM recognition during the reaction turnover. In addition, the SAM binding site accommodates a sulfate and a glycerol, offering structural information to initiate structure-based drug design. Altogether, these results contribute to a better understanding of theFlavivirusmethyltransferases, which are central players in the virus replication.
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Coutard
authors.affiliation: Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Barral
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Lichière
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France.
authors.forename: Barbara
authors.initials: B
authors.lastname: Selisko
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France.
authors.forename: Baptiste
authors.initials: B
authors.lastname: Martin
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France.
authors.forename: Wahiba
authors.initials: W
authors.lastname: Aouadi
authors.affiliation: Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix-Marseille Université, Luminy Campus, Marseille, France.
authors.forename: Miguel Ortiz
authors.initials: MO
authors.lastname: Lombardia
authors.affiliation: IBMM, UMR 5247 CNRS, Université de Montpellier, ENSCM, Department of Nucleic Acids, Montpellier, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Debart
authors.affiliation: IBMM, UMR 5247 CNRS, Université de Montpellier, ENSCM, Department of Nucleic Acids, Montpellier, France.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Vasseur
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France.
authors.forename: Jean Claude
authors.initials: JC
authors.lastname: Guillemot
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Canard
authors.affiliation: Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France Etienne.Decroly@afmb.univ-mrs.fr.
authors.forename: Etienne
authors.initials: E
authors.lastname: Decroly
mesh_terms: D000495:Allosteric Site; D000998:Antiviral Agents / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D015195:Drug Design; D004926:Escherichia coli; D006860:Hydrogen Bonding; D008780:Methyltransferases / Q000096:biosynthesis / Q000737:chemistry*; D008958:Models, Molecular; D011485:Protein Binding; D017361:Viral Nonstructural Proteins / Q000096:biosynthesis / Q000737:chemistry*; D000071244:Zika Virus / Q000201:enzymology*
chemical_list: D000998:Antiviral Agents; D017361:Viral Nonstructural Proteins; D008780:Methyltransferases
keywords: RNA processing; Zika virus; flavivirus; methyltransferase; protein structure-function