Figure 2
From: The essential inner membrane protein YejM is a metalloenzyme
Location of novel metalloenzyme YejM active site and substrate sites. (a) YejMPD with putative magnesium ion (Mg2+) (green) in a larger vestibule at active site below layer II and III. (b) Active site of YejMPD-F349A with conserved threonine Thr302 (deep purple) from layer III, putative Mg2+ shown by 2Fo-Fc density map (green mesh) at sigma level 2.5, Thr301, Thr302, Asp303, Asp268, Asn403, and Arg451 with 2Fo-Fc electron density (light blue mesh) at sigma level 1.5. (c) Active site of YejMPD-F349A with conserved threonine Thr302 (deep purple) from layer III, other residues involved in Mg2+ (green sphere) and substrate ethanolamine (ETA) are Asp268, Asn403, Arg451 and His468, prospective specific waters (red spheres). (d) Active site of MCR-1 around zinc (Zn2+, blue sphere) include conserved phosphorylated threonine TPO70, Glu31, Thr32, His180, Asp250, His251, His263. (e) Active site of EptA around Zn2+ include conserved threonine Thr280, Glu240, Asp324, His383, His453 and His465. (f) Active site of LtaS with conserved threonine Thr300 (deep purple) from layer III involved in coordination of manganese (Mn2+, purple sphere) and substrate 1,2-Etheanediol (EDO) in stick representation orange, together with residues Glu255, Asp475, His253, Trp354, Arg356, His476. (g) Front view of YejMPD-F349A, black arrow pointing towards the additional density observed in the Fo-Fc map (ED) at 2.2 sigma level (green mesh), located at interface between layer III and the CT domain. (h) YejMPD side view. (i) YejMPD back view. (j) Electrostatic surface presentation of YejMPD side view and cropped in Z plane to show large negatively charged pocket with additional Fo-Fc map (green mesh). (k) Zoom in on the negatively charged pocket lined by residues Leu288, Asp490, Asp493, Gln514 and Glu580. Dummy atoms (light blue spheres) placed into the pocket surrounded by the electrostatic surface overlaid in mesh and solid representation. (l) Electrostatic surface of YejMPD back and side views. Black arrows points towards positively charged access funnels (port 1) and (port 2) towards the visible Fo-Fc density (green mesh), indicating its accessibility from the outside.
