Fig. 4: ImcA is DGC protein with a six-TM domain.
From: A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa
a ImcA homo-dimeric apo form predicted by AlphaFold2 (left) and its substrate analog GMPCPP-bound form (Cryo-EM, right). The secondary structure units are defined by DSSP-Stride plugin in PyMOL. And the ligand was represented with ball-and-stick, and further colored by element (N: blue, O: red, C: white, P: orange). b There is a symmetric contact interface between TM domains. The 2-fold rotation axis is indicated by a black solid ellipse and the same below. The residue labels are composed successively of the single-letter identifier of certain amino acid and corresponding residue number, and colored in the same color with corresponding chain. c Details of the dimeric catalytic domains with the secondary structure units of each chain colored in corresponding color. The sidechains of amino acids situated in the vicinity of catalytic pocket are displayed with stick. Moreover, the GGEEF motif and identified D-riched motif are colored in yellow and blue, respectively. d Enlarged details of single ImcA DGC catalytic domain located in GMPCPP-bound dimeric form with the electron density map for GMPCPP (8.0σ) shown in light blue meshes. e Enlarged details of the membrane-proximal ligand binding pocket with the electron density map for GMPCPP (6.5σ) shown in light blue meshes.
