Structure and Function of Caliciviral RNA Polymerases

Figures

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  Figure 1. Diagrammatic representation of Caliciviridae genome. The 3′ end poly (A) tail and the 5′ end covalently linked virion protein genome-linked (VPg) depicted as (A)n and a gray circle, respectively. In sapo-, lago-, and neboviruses, open reading frame 1 (ORF1) and open reading frame 2 (ORF2) are used, whereas ORF1, ORF2 and ORF3, with an additional ORF4 for murine norovirus (MNV), are used in noro- and vesiviruses. Non-structural viral proteins are described below in a box.

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  Figure 2. Superimposed structures of calicivirus RNA-dependent RNA polymerases (RdRps) based on 480 Cα atoms. The crystal structures of the rabbit haemorrhagic disease virus (RHDV), human norovirus (HuNoV), sapovirus (SaV), and MNV RdRps are shown in a wireframe representation, coloured in sky blue, orange, green, and black, respectively. The active site and the N- and C-terminal regions are shown in yellow and in circles, respectively.

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  Figure 3. Details of the superimposed active sites of RdRps. (a) Structures of the apoenzyme with catalytic Asp in the motifs A and C and divalent metal ions (Mn2+) (upper panel), the RNA/NTP-incorporated (middle), showing incoming NTP (CTP), and the backtracked state (lower panel), showing elongated RNA after incorporation of NTP with Mn2+ in the HuNoV RdRp. The RdRp structures of RHDV (1KHW), HuNoV (1SH0, 3BSO and 4QPX), and MNV (3QID) were used for superposition; (b) The top view of superimposed HuNoV RdRp structures shows flexible thumb movement during RNA synthesis in a dotted box, with template, primer, and NTP. The apo and RNA-bound structures are shown below.

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  Figure 4. The C-terminal region of the apo and RNA-bound RdRps from HuNoV and SaV. The C-terminal region is coloured in red and cyan in HuNoV (upper panel), and the swapped C-terminal is shown in SaV RdRp, coloured in green and orange (lower panel).

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  Figure 5. Structures of the RdRp-VPg complexes. (a) Superposition of the RdRp–VPg complex structures from foot and mouth disease virus (FMDV), coxsackievirus (CV), and enterovirus 71 (EV71) in picornaviruses. FMDV VPg is bound at the active site, while CV VPg is at the junction of the palm and thumb and EV71 VPg is bound at the bottom of the palm. In the box below, caliciviral and picornaviral VPg structures are shown; (b) Multimerization of the PV and FMDV RdRps. Cryo-electronmicroscopy (EM) reconstructed or negative-stained transmission electron microscopy (TEM) images of RdRps (upper panel) and the interactions of RdRp molecules in the crystal lattices (lower panel). PV and FMDV RdRp fibril images are adopted from Electron Microscopy Data Bank (EMDB) and [43], respectively.