RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli - PubMed (original) (raw)

Multiple sequence alignment of eight diverse MTTases (two from each of the four subfamilies): RimO_Eco (YliG/RimO from E. coli K-12; NP_415356), RimO_Aae (aq_849 from Aquifex aeolicus; NP_213577), MiaB_Eco (MiaB from E. coli K-12; NP_415194), MiaB_Aae (aq_284 from A. aeolicus; NP_213198), YqeV_Bsu (BSU25430/YqeV from B. subtilis; NP_390421), YqeV_Aae (aq_474 from A. aeolicus; NP_213332), Mj08_Mja (Mj0867 from M. jannaschii; NP_247862), Mj08_Hsa (CDKAL1 from Homo sapiens; NP_060244). The three domains as defined by Pfam are boxed, inclusive of edges: UPF0004 (pink), radical-SAM (cyan), and TRAM (brown). Residues conserved in the larger alignment, listed in

SI Table 2

, are boxed in black, and additional residues conserved in all eight sequences in this alignment are boxed in gray. (For this purpose, the following residues are treated as equivalent: S = T, E = D, K = R, F = W = Y, and I = L = V.) Subfamily-specific residues as defined in

SI Table 3

are boxed in the color of the subfamily that differs from the remaining three: blue for RimO, red for MiaB, green for YqeV, and yellow for Mj0867. The three cysteines that coordinate the [4Fe-4S] cluster in the radical-SAM domain of MiaB are indicated by *, the three cysteines that coordinate the [4Fe-4S] cluster in the UPF0004 domain of MiaB are indicated by §, and residues that may be involved with SAM binding (see

SI Table 2

) are indicated by †. The NPPY motif conserved among eukaryotic Mj0867 members is boxed in yellow. At the lower right is a schematic phylogenetic tree, based on

SI Fig. 5

, showing the relationships of these sequences to one another.