Variable Macro X Domain of SARS-CoV-2 Retains the Ability to Bind ADP-ribose

David N. Frick; Rajdeep S. Virdi; Nemanja Vuksanovic; Narayan Dahal; Nicholas R Silvaggi

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.31.014639 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.31.014639 doi: bioRxiv preprint FIGURE 4. The SARS-CoV-2 macro X domain structure. (A) The electron density is shown for a representative portion of the structure (residues 359-361) on the surface of the protein. The 2mFo-DFc map is contoured at 1.5σ and is shown as a magenta mesh. The mFo-DFc (difference) maps are shown at + and -3.0σ as green and red mesh, respectively. (B) Ribbon diagram of the SARS-CoV-2 macro X domain structure colored according to the sequence conservation plot in Figure 2 as a gradient from red (low conservation; <10%) to blue (highly conserved; 100%) through magenta. As can be seen in the sequence alignment, the N-and C-termini are particularly poorly conserved. (C) Overlay of the structure of the SARS-CoV-2 macro X domain bound to ADP-ribose determined by Michalska et al. of the CGSID (PDB ID 6W02) with the ultra-high-resolution structure of the unliganded protein determined here. ADP-ribose is shown in ball-and-stick with the carbon atoms colored gold. The backbone trace of the unliganded structure is colored cyan, and that of the ADP-ribose-bound model is colored grey. There are three loops with significantly different conformations in the two structures. In the unliganded structure, the β2-α2 loop is colored bright red, the β4-α4 loop is colored purple, and the β5-α5 loop is colored bright green. The same regions of the ADP-ribose-bound structure are colored pale red, pale purple, and pale green, respectively. The transparent blue and yellow spheres represent water molecules bound to the unliganded (transparent blue) and ADP-ribose-bound (transparent yellow) forms of the protein. Interestingly, several of the water molecules interacting with ADP-ribose in 6W02 can also be found in the unliganded structure of the protein. The inset shows a close-up of the boxed region colored according to the same scheme. The β2-α2 and β5-α5 loops, which contact ADPribose, are shown in ball-and-stick. Note that the β2-α2 loop rotates ~180° to allow it to make a hydrogen-bonding interaction with the 1'-hydroxyl of the ribose moiety. Also, the phenylalanine residue in the β5-α5 loop (F336) would clash with the β-phosphate and ribose of ADP-ribose if the β5-α5 loop did not adopt a different conformation. author/funder. All rights reserved. No reuse allowed without permission.