Fig. 2. Structural features of EmbB.

a Electrostatic representation of EmbB, with a zoom-in around the putative active site, labeled according to where the substrates are likely to bind, where red is more negatively charged and blue more positively charged. A comparison with the PglB active site with bound substrates is also shown, after PglB was aligned against EmbB. b Structure of EmbB, rendered in cartoon and colored based on ConSurf⁶⁹ score for sequence conservation. The more negative the score, the more conserved the residue. The putative active site cavity, generated by the Voss Volume Voxelator server⁶⁸ is colored in semi-transparent green. The insert shows the putative active site cavity with the strictly conserved residues labeled. c EmbB (pale blue) is superimposed on PglB (semi-transparent yellow), with the ligands and Mn²⁺ ion of PglB shown in yellow as sticks and a ball, respectively. d Residues that are known to maintain catalytic activity while altering substrate specificity on a loop between TM13 and TM14 are labeled and side chains are shown. e A tightly bound phosphatidylglycerol (PG shown as ball-and-stick) and calcium ion (shown as a ball) in a pocket between TM2, JM1, and β10 is shown. The density map of the lipid and the ion is displayed as mesh. f Glycan ligands for the top ten Dali server hits for both N-CBM and C-CBM were mapped onto the structure as a gray ball representation. 2WJS [10.2210/pdb2WJS/pdb] (PDB ID) was used for N-CBM, while 3PTY [10.2210/pdb3PTY/pdb] and 4GWM [10.2210/pdb4GWM/pdb] were used for the C-CBM. The missing loop in EmbC is colored in red, and the insert is a zoomed-in view. Sequence alignment of the region around the loop is appended below the insert. The putative sugar acceptor entry pathway is shown as an orange dotted line.