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. 2022 Mar 14;11:e76107. doi: 10.7554/eLife.76107

Figure 2. Conformational changes in the glutamate kinase (GK) domain-binding pocket.

(A) GK domain of the P5CSGlu filament, with glutamate shown as sticks with yellow carbons. The dashed lines represent disordered segments (residues 124–142, 211–232, and 275–297) in this model. (B) GK domain of the P5CSMix filament, with G5P, Mg+, and ADP shown as sticks with pink, green, and red carbons, respectively. The dashed lines represent disordered segments (residues 128–140, 214–228, and 282–295) in this model. (C, D) GK domain model surface representation showing the conformation of the binding pocket in the P5CSGlu filament or P5CSMix filament. The cryo-electron microscopy (cryo-EM) density of binding glutamate molecule in (C), and the binding complex of G5P, Mg+, and ADP in (D). The dashed lines represent ‘open loop’ and ‘closed loop’

Figure 2.

Figure 2—figure supplement 1. Structural details of the glutamate kinase (GK) domain characterized.

Figure 2—figure supplement 1.

(A) The comparison of E. coli GK structure without PUA domain (tan; PDB: 2J5V) and Drosophila GK domain structure of P5CS (blue-violet; this study), with 30.56% sequence identity and root-mean-square-deviation (RMSD) value of 1.363 Å (198 atom pairs). (B) Cryo-electron microscopy (cryo-EM) map quality of the GK domain active site in the P5CSMix filament (blue-violet), indicating that the conformation of bound G5P/ADP (green) is better than Glu/ATP (dark yellow). (C) Unmodeled ligand densities in the GK domain of the P5CSGlu/ATPγS filament. (D) Superimposition between the GK domain protomer or tetramer structure of the P5CSGlu/ATPγS filament (coral) and that of the P5CSMix filament (blue-violet). (E) The binding mode of glutamate (yellow) and G5P (pink) in the GK domain.