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

The Ca atoms of domains 1A and 2A of free nsp10Á and the nsp10Á-DNA complex can be superimposed with an RMSD of 0.6 Å , indicating that the relative orientations of these core domains are barely affected by DNA binding ( Figure 6A ). However, outside these domains, the effect of DNA binding was considerable, with the RMSD between the Ca atoms of the two forms of nsp10Á increasing to 1.8 Å . Particularly large conformational changes were observed in domain 1B, which rotates $28 towards ZBD in the nsp10Á-DNA complex ( Figure 6A ). The RMSD between the Ca atoms of the two forms of domain 1B is 1.8 Å , with loop residues being affected most profoundly (Supplementary Figure S6A) . Both width and height of the polynucleotide substrate channel formed by domains 1A and 1B (originally $5 and 11 Å , respectively) are increased by 2 Å on this rotation. This reorganization makes this channel large enough to accept single-stranded nucleic acids, although it remains too narrow for a nucleic acid duplex ( Figure 6B ). Consequently, double-stranded nucleic acids must be unwound at the entrance of the substrate channel to let a single-stranded chain enter. Besides this large conformational change, temperature factor calculations suggest that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible (Supplementary Figure S2) . For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding ( Figures 2C and 3B and Supplementary Figure S2 ).