Figure 3.

Structure and evolution of PylRS and the Pyl operon. (A) Key hydrogen-bond interactions in the active site of M. mazei PylRS with pyrrolysyl-adenylate (Pyl-AMP) bound. (B) Two views of the D. hafniense PylRS/tRNA^Pyl complex showing the tRNA binding domain 1 (cyan), the catalytic core domain (tan), the bulge domain (yellow), the C-terminal tail domain (green), and α-helix 6 (blue) emerging from the other protomer (gray). The tRNA core binding surface (magenta highlight) and U shaped concave surface (purple highlight) are also illustrated. Pyl-AMP from the M. mazei PylRS structure was superimposed onto the DhPylRS structure for reference. (C) The PylRS maximum likelihood phylogenetic tree includes all known putative Pyl-decoding organisms to date, and the organization of the Pyl operon in each genome sequence is shown adjacent to the tree. Square brackets indicate partial sequence data from a short sequence read, and curly brackets indicate that the Pyl operon is split between different contigs from a metagenomic survey. * indicates an in-frame TAG codon. Sequence data were downloaded from the Integrated Microbial Genomes database [65]. The tree was calculated with PHYML [66] using a BioNJ starting tree and SPR tree search followed by NNI branch swapping to optimize the tree. All alignment positions were considered, likelihood parameters were estimated from the alignment, and the JTT+Γ model with 8 rate categories was applied. Bootstrap values (only those > 50 are shown) were computed according to the Shimodaira-Hasegawa re-estimation of log-likelihood test implemented in PHYML.