Crystal structure of Middle East respiratory syndrome coronavirus helicase

Hao, Wei; Wojdyla, Justyna Aleksandra; Zhao, Rong; Han, Ruiyun; Das, Rajat; Zlatev, Ivan; Manoharan, Muthiah; Wang, Meitian; Cui, Sheng

It has been previously shown that CoV nsp13 interacts with both RNA and DNA in a sequence-independent manner [29, 35, 36] . To analyze the nucleic acid binding pocket of MERS-CoV nsp13, we generated a model of nsp13-ssRNA based on the superposition of the helicase domain of nsp13 with the helicase domains of hUpf1, scUpf1 [26] and EAV nsp10 [25] . The model shows that while the 3' end of single-stranded RNA is located in the channel formed by 1B, Stalk and RecA1 domains; the 5' end of the RNA lies on top of RecA2 domain (Fig 6A) . Although the helical insertion equivalent to the Upf1 1C domain is missing in nsp13, the protein has a topologically equivalent loop between β17 and β18 which fulfills similar function in RNA binding. The β17-β18-loop makes direct contacts with 1B domain, forming the 3' end outlet of the putative RNA binding channel. The narrowest opening of the putative RNA binding channel has the width and height of 6 and 12Å, which is just enough to accept a single-stranded RNA or DNA (Fig 6B) . The dimension of the RNA binding channel of nsp13 is similar to that in EAV nsp10, but smaller than the channel in Upf1. Based on structural Crystal structure of MERS-CoV nsp13 comparisons, we predicted the residues of nsp13, which are likely involved in RNA recognition (S2 Fig & S1 Table) . Their structural equivalents are mostly conserved in EAV nsp10 and Upf1 helicases, suggesting that CoV nsp13 adopts the similar mechanism for nucleic acids binding.