The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes

Tan, Jinzhi; Vonrhein, Clemens; Smart, Oliver S.; Bricogne, Gerard; Bollati, Michela; Kusov, Yuri; Hansen, Guido; Mesters, Jeroen R.; Schmidt, Christian L.; Hilgenfeld, Rolf

We have used automatic docking procedures to place the Gquadruplex found in the bcl-2 promoter region ( [33] ; PDB code 2F8U) into our crystal structures. One potential binding site identified is in the cleft between the SUD-M and the SUD-N subdomains within the SUD core dimer ( Figure S2A ); this binding site is spatially close to the mutations M3 and M4, consistent with the observation that these mutations abolish binding completely. However, we have previously shown by Dynamic Light-Scattering that G-quadruplex binding leads to oligomerization of SUD core [31] . Consequently, we have also constructed models based on the packing modes of SUD core dimers observed in our crystal structures. One potential binding site for G-quadruplexes might be in a cleft between two consecutive SUD core dimers as they occur in both the monoclinic and triclinic crystal forms ( Figure S2B ), but for confirmation, any of these models will have to await crystallographic determination of the complex. In summary, our mutation experiments demonstrate an involvement of several of the many lysine residues of SUD in binding G-quadruplexes, but as it is probably extended surfaces of SUD core oligomers that participate in this process, it is not possible to pinpoint any single amino-acid residue.