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

At present, it is completely unclear whether and how the individual domains of Nsp3 interact with one another or with other components of the coronaviral replicase complex. Also, some of them possibly recognize proteins of the infected host cell [2] . In the absence of functional data on these domains, attempts have been made to derive their possible biological role from their three-dimensional structures (see [3] for a review). The NMR structure of an N-terminal fragment of the acidic domain (Nsp3a) has revealed a ubiquitin-like fold complemented by two additional short a-helices ( [4] , PDB code 2IDY). NMR chemical-shift analysis suggested that these non-canonical structural elements might bind single-stranded RNA with some specificity for AUAcontaining sequences, although the K D values observed are relatively high (,20 mM). Interestingly, a second ubiquitin-like domain occurs in Nsp3, as part of the papain-like proteinase (PL2 pro , Nsp3d, [5] ; PDB code 2FE8). The PL2 pro cleaves the viral polyprotein after two consecutive glycine residues to release Nsp1, Nsp2, and Nsp3, respectively (The remaining cleavage reactions are performed by the coronaviral main proteinase (M pro ; [6-8]) ). In addition to its proteolytic activities on the N-terminal third of the polyproteins, the SARS-CoV PL2 pro has also been shown to be a deubiquitinating enzyme [9] [10] [11] [12] . Lindner et al. [13] have shown that in addition to its proteolytic and deubiquitinating activity, the SARS-CoV PL2 pro acts as a de-ISGylating enzyme. Induction of ISG15 and its subsequent conjugation to proteins protects cells from the effects of viral infection [14, 15] . Since the ISG15 gene is induced by interferon as part of the antiviral response of the innate immune system, the de-ISGylation activity of Nsp3d could explain the suppression of the interferon response by the papain-like protease, in addition to a possible direct interaction between the PL2 pro and IRF3 [16] .