Fig. 2: Binding modes of RNA cap analogues and SAM and mechanism of methyl transfer.
From: Structural basis of RNA cap modification by SARS-CoV-2
a Overlay of a binary (S-adenosyl methionine or SAM-bound; gray cartoons) and ternary (SAM, RNA cap-bound; light cyan cartoons) complexes shows outward motions (green arrows: 7 Å in gate loop 1, and 5.2 Å in gate loop 2) after RNA cap binding to nsp16. RNA cap, red stick; SAM in ternary complex, blue stick; SAM in binary complex, gray stick. b green sticks; nsp16 residues that interact with RNA cap. c magenta sticks; nsp16 residues that contact with SAM. d A close-up view of Cap-nsp16 interactions reveals a network of hydrogen bonding with successive phosphates, me7GO and A1 nucleotides of cap. Water, gray spheres, h-bonds, black dashed lines. e A water (yellow sphere) coordinates with the target 2′-O atom of A1, and catalytic tetrad residues and N43. The methyl group of SAM is positioned for direct in-line attack from the 2′-O. f Binding isotherms and fitting of data for nsp16 binding to RNA cap-0 (me7GpppA), cap-1 (me7GpppAm) analogues, and SAM. Each data point represents average of two independent experiments (n = 2). g The 2′-O methyltransferase activity measured as percentage of Cap-0 to Cap-1 conversion is plotted against nsp16/nsp10 protein concentration. Higher enzymatic activity is observed on an RNA substrate with A (red circles) as the target base for 2′-O methylation (N1), compared to an identical RNA but with G (black square) as N1 or initiating nucleotide. Results are average of three independent experiments (n = 3) with one standard deviation (s.d.) for each RNA shown as error bars. Source data are provided as a Source Data file. h Guanine base (yellow stick) is modeled at N1 position of cognate adenine (red stick). The N2 amine of guanine intrudes into the SAM pocket and may be repelled by positively charged sulfur of SAM (blue stick).
