Mechanism of 3′-Matured tRNA Discrimination from 3′-Immature tRNA by Class-II CCA- Adding Enzyme  Seisuke Yamashita, Kozo Tomita  Structure  Volume 24, Issue 6, Pages 918-925 (June 2016) DOI: 10.1016/j.str.2016.03.022 Copyright © 2016 Elsevier Ltd Terms and Conditions

Structure 2016 24, 918-925DOI: (10.1016/j.str.2016.03.022) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 Complex Structure of TmCCA and tRNA_CCA (A) Overall structure of the complex of T. maritima CCA-adding enzyme (TmCCA) and tRNA with a 3′-CCA end (tRNA_CCA). The head, neck, body, and tail domains are colored magenta, green, blue, and orange, respectively. tRNA_CCA is colored gray. Electron densities of tRNAs. Overall complex structure of the class-I Archaeoglobus fulgidus CCA-adding enzyme with tRNA_CCA (inset, Xiong and Steitz, 2004; PDB: 1SZ1). The 2Fo–Fc map (colored blue) of the 3′-region of tRNA_CCA in the complex structure, contoured at 0.8 σ. (B and C) Detailed view of interactions between TmCCA and tRNA_CCA. (D) Schematic presentation of the interactions between tRNA_CCA and TmCCA in the complex. See also Figure S1. Structure 2016 24, 918-925DOI: (10.1016/j.str.2016.03.022) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 Structural Change of TmCCA Upon tRNA_CCA Binding (A) Superimposition of the structures of apo TmCCA (Toh et al., 2009; PDB: 3H38, colored gray) and TmCCA complexed with tRNA_CCA (colored as in Figure 1A). (B) Stereo view of the superimposition of the head domain structures of apo TmCCA and TmCCA complexed with tRNA_CCA. The β hairpins between β4 and β5 and the loops connecting β6 and α5 are colored orange and yellow in the structure of the TmCCA: tRNA_CCA complex for clarity, and the corresponding β hairpin and loop in apo TmCCA are colored dark gray. (C) Stereo view of the tail domain structures of apo TmCCA and TmCCA complexed with tRNA_CCA. The TΨC and D loops of the tRNA are colored yellow and light blue, respectively. Structure 2016 24, 918-925DOI: (10.1016/j.str.2016.03.022) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 Structure of the Active Pocket of the TmCCA: tRNA_CCA Complex (A) Stereo views of the superimposition of the TmCCA: tRNA_CCA complex (colored blue) onto the AaL: tRNA_CCA complex (colored magenta). For clarity, tRNAs are depicted by ribbon models, and enzymes are shown transparently. (B) Stereo view of the catalytic core structure of the TmCCA: tRNA_CCA complex. Schematic representation of the catalytic core structures in the TmCCA: tRNA_CCA complex. (C) Stereo view of the catalytic core structure of the AaL: tRNA_CCA complex (Yamashita et al., 2015). Schematic representation of the catalytic core structures in the AaL: tRNA_CCA complex. (D) Superimposition of the catalytic core structures in (B) and (C). The 3′-parts of tRNA_CCA in TmCCA (colored cyan) and AaL (colored magenta) are shown by stick models, and only the structure of TmCCA is shown in gray, for clarity. See also Figure S2. Structure 2016 24, 918-925DOI: (10.1016/j.str.2016.03.022) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 4 Mechanism of Recognition and Discrimination of Mature tRNA Schematic representation of the mechanism of 3′ end recognition and discrimination by a class-II CCA-adding enzyme. The tRNA-binding modes (left) and structures of the active pockets (right) are shown. (A) The 3′ end of tRNA lacking 3′-A76 (tRNA_CC) at the release/discrimination site. This state is unstable, and the 3′ end relocates to the catalytic site shown in (B), as indicated by the bold arrow. (B) The 3′ end of tRNA_CC at the catalytic site (left; pre-A76-addition stage). The 3′ end of 3′-mature tRNA (tRNA_CCA) at the catalytic site (right; post-A76-addition stage). (C) The 3′ end of tRNA_CCA at the release/discrimination site. The active site and the release/discrimination site in the active pockets are enclosed by dashed circles. See also Figures S3, S4, and Movie S1. Structure 2016 24, 918-925DOI: (10.1016/j.str.2016.03.022) Copyright © 2016 Elsevier Ltd Terms and Conditions