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. 2021 Feb 23;7(3):476–487. doi: 10.1021/acscentsci.0c01285

Figure 4.

Figure 4

Crystal structures of EcYihV SF kinase. (a) Kinetic plots showing effect of metabolites on EcYihV-catalyzed phosphorylation of SF to SFP at [ATP] = 1.0 mM. (b) (Left) EcYihV dimer in complex with AMPPNP·Mg in open and closed conformations is shown in ribbon with the two subunits shown in coral and blue. Each subunit is composed of two-domain architecture with α/β nucleotide binding domain and β-sheet “lid” domain. (Right) Lid domains of the dimer form a β-clasp dimerization motif that serves both structural and catalytic roles. (c) Close-up view of EcYihV·AMPPNP·Mg showing nucleotide binding site in the closed conformation. (d) EcYihV·SFP complex structure and active site interactions with bound SFP product molecule. (e) Close-up view of EcYihV·ADP·Mg·SF active site showing hydrogen bonding interactions in a quaternary complex. Backbone and carbon atoms of subunits A and B are shown in coral and blue, respectively, and ADP, AMPPNP, SF, and SFP are shown in cylinder format. Electron density corresponds to the 2Fo – Fc and in blue at levels of 1σ for c–e. (f) Cartoon of ligand binding pocket of EcYihV·ADP·Mg·SF complex depicting hydrogen bonding interactions with active site residues.