Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase

Deng, Zengqin; Lehmann, Kathleen C.; Li, Xiaorong; Feng, Chong; Wang, Guoqiang; Zhang, Qi; Qi, Xiaoxuan; Yu, Lin; Zhang, Xingliang; Feng, Wenhai; Wu, Wei; Gong, Peng; Tao, Ye; Posthuma, Clara C.; Snijder, Eric J.; Gorbalenya, Alexander E.; Chen, Zhongzhou

Next we analysed the existence of structural similarity between EAV nsp10Á and other proteins by scanning a protein data bank using the DALI server (51) . The structure of the nsp10Á HEL1 domain was found to be most similar [Z score, 20.9; root-mean-square deviation (RMSD), 3.5 Å ] to the helicase core of nonsensemediated mRNA decay factor Upf1 and its homolog Ighmbp2 (Z score, 19.9; RMSD, 3.0 Å ), which both belong to the Upf1-like helicase subfamily (11) . Further comparisons revealed that this resemblance extends into the respective N-terminal ZBDs: the binuclear RING-like module of nsp10Á ZBD was found to be most similar to RING-like module 1 in the CH-domain of Upf1 ( Figure 4E ). This similarity was rather limited (Z-score of 1.9 and RMSD of 2.2 Å ) because only six out of the eight Znchelating residues in the two domains could be juxtaposed ( Figure 4F ) and because loops L1, L3 and helix a1 in nsp10Á are shorter than the corresponding elements in Upf1. We did not detect significant similarity of the treble-clef zinc finger with other proteins, although we note that the Upf1 CH-domain also has a zinc finger (but of a different fold) downstream of the RING1 module. Thus, EAV nsp10 ZBD prototypes a novel and complex multi-domain zinc finger with distinct structural properties. On the other hand, EAV nsp10 and Upf1 share a similar domain organization, including structurally similar RING and helicase domains. These similarities are further enhanced by the 5 0 -3 0 directionality of duplex unwinding shared by both these helicases and likely extends to other nidovirus helicases in view of the observed sequence conservation (Supplementary Figure S3B ).