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. 2015 Oct 12;112(43):13348–13353. doi: 10.1073/pnas.1505271112

Fig. 2.

Fig. 2.

Mechanism of alarmone synthesis. (A) Three regions of SAS1 (R1–R3) show different dynamic responses to the presence of different nucleotides in HDX experiments after 30 s of deuteration. The graph shows the percentage of HDX of R1 (red), R2 (green), and R3 (blue) in the presence or absence of different nucleotides. Error bars represent the SD of three independent measurements. (B) Location of R1 (red), R2 (green), and R3 (blue) on the crystal structure of an SAS1-AMPCPP monomer. An arrow indicates AMPCPP within the active site. (C) The ATP (pale green ball) and GDP or GTP (dark green triangle) substrates bind to the active site of SAS1 (blue) in sequential order. The transition state of the reaction is indicated by a double dagger (‡). The products (p)ppGpp and AMP are shown as orange and gray balls, respectively. (D) ATP (mimicked by AMPCPP, deep teal) binds in a tense, U-shaped conformation in the active site of SAS1. Dashed lines indicate interactions between residues of SAS1 and AMPCPP. The magnesium ion is shown as a green sphere. (E) Superimposition of the active sites of SAS1 bound to AMPCPP (deep teal) and RelA bound to GDP (green). The attacking 3′-OH group of the ribose of GDP is encircled in black, and the arrow indicates the direction of nucleophilic attack toward the β-phosphate of AMPCPP. (F) Scheme of the catalytic mechanism of alarmone synthesis. A detailed description is given in the text.