Fig. 3: Structural studies (empirical and predicted) of the full-length CdaA in lipid nanodiscs.
From: Membrane-embedded CdaA is required for efficient synthesis of second messenger cyclic di-AMP
A Alphafold 2 multimer prediction of full-length CdaA in surface representation. The side view of the predicted tetrameric full-length CdaA complex. The lipid environment is indicated with thick grey lines. The flexibility of each inactive DAC-dimer is indicated with arrows and transparent hemispheres. The bottom view highlights the opposing inactive DAC-dimers in proximity while attached to the transmembrane domain via a linker. The proximal active sites of the opposing DAC-dimers (teal) are facing towards each other. Representative 2D class averages of each stage are displayed below each panel. B Alphafold 3 prediction of the full-length CdaA in the presence of ligands (Mn-AMP). The ‘proximal’ active sites are engaged head-to-head orienting the two AMPs in a conformation that closely resembles cyclic di-AMP (dashed line). C Alphafold 2 multimer prediction of the full-length CdaA complex inhibited by GlmM. Representation is the same as in (A). The GlmM protomers are displayed in light brown and gray respectively. Representative 2D class averages of each stage are displayed below each panel. D Cryo-EM density map of the inactive DAC-dimer of CdaA bound to GlmM with the respective model (PDB:9G69) represented in ribbons. The two protomers of the catalytic DAC domain are coloured in teal and green respectively for clarity. Similarly, promoters of the GlmM complex are shown in light brown and light grey. The flexible domain 4 of GlmM is indicated in a grey ellipse. E A closer view of the inactive DAC-dimer of CdaA is displayed in ribbons. The active sites are situated in opposing sides of the inactive DAC-dimer (indicated by arrows). F A closer view of the active site of the catalytic domain (teal). The catalytic residues, D184GA and R216HR are coloured in yellow and orange respectively. A density (mesh) that corresponds to bound Mn-ATP is present in the active site (ligand fitted from homologue (PDB:4RV7) from L. monocytogenes).
