Extended Data Figure 4: Conformational changes in MraYAA that create binding pockets for the uridine and 5-aminoribosyl groups of MD2.
From: Structural insights into inhibition of lipid I production in bacterial cell wall synthesis
a, A close-up view of apoMraYAA with key residues that participate in conformational changes upon MD2 binding shown as sticks in various colours. b, A close-up view of the nucleoside-binding pocket in the MraYAA–MD2 complex with MD2 omitted. Key residues are coloured as in a. c, A close-up view of the interactions MD2 (green) makes with the nucleoside-binding pocket of MraYAA. Interactions between MraYAA and MD2 are shown as dotted lines. It is noteworthy that residues interacting with the uridine moiety of MD2 move large distances (5–17 Å for residues Lys70, Asp196, Asn255 and Phe262), while the residues binding the 5-aminoribosyl group of MD2 (Thr75, Asn190 and Asp193) do not make large side-chain movements after MD2 binding. The uridine and 5-amino ribosyl groups of MD2 are circled. d, Interactions between the uracil base of MD2 (green) and the nucleoside-binding pocket of MraYAA. The uracil base forms H-bonds with side chains of Asn255, Asp196 and Lys70 and forms a π–π interaction with Phe262. d, The 5-aminoribosyl group of MD2 forms H-bond interactions with side chains of Thr75, Asn190 and Asp193, and the backbone amide of Gly264.
