Volume 16, Issue 7, Pages 1095-1104 (July 2008) The tRNA-Induced Conformational Activation of Human Mitochondrial Phenylalanyl- tRNA Synthetase  Liron Klipcan, Inna Levin, Naama Kessler, Nina Moor, Igal Finarov, Mark Safro  Structure  Volume 16, Issue 7, Pages 1095-1104 (July 2008) DOI: 10.1016/j.str.2008.03.020 Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 1 The Structure of Human mitPheRS (A) Overall structure of the human mitPheRS enzyme. The N-terminal region (residues 1–47) is depicted in yellow, the catalytic domain (residues 48–289) in blue, the linker region (residues 290–322) in red, and the C-terminal domain (residues 323–415) in green. (B) A structure-based sequence alignment of the catalytic domain of human mitPheRS with those of mit yeast, T. thermophilus (PDB code: 1pys), and E. coli PheRSs. Conserved and similar residues are highlighted in red. The secondary structural elements, as found in the crystal structure of mitPheRS, are indicated above the sequence alignment. Conserved motifs of class II synthetase are highlighted by boxes. (C) A structure-based sequence alignment of the C-terminal domain of human mitPheRS. Amino acid residues that participate in specific tRNAPhe anticodon recognition by T. thermophilus ABD are marked by arrows. Structure 2008 16, 1095-1104DOI: (10.1016/j.str.2008.03.020) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 2 Structure Comparison of Human mitPheRS with Other Class II aaRSs (A) Superposition of the catalytic core of mitPheRS and CAM of T. thermophilus (PDB code: 1pys). MitPheRS is colored blue and CAM is colored red. (B) Superposition of the catalytic cores of mitPheRS and PylRS from Methanosarcina mazei (PDB code: 2q7e). MitPheRS is colored blue and PylRS is colored green. (C) Comparison of the catalytic cores of human mitPheRS and CLM of T. thermophilus (PDB code: 1pys). MitPheRS is colored blue and CLM is colored pink. (D) Comparison of the catalytic cores of human mitPheRS and SepRS from Archaeoglobus fulgidus (PDB code: 2du3). MitPheRS is colored blue and SepRS is colored yellow. (E) Comparison of the C-terminal domain of human mitPheRS and the ABD (B8∗) of T. thermophilus (PDB code: 1pys). MitPheRS is colored blue and B8∗ of T. thermophilus is colored red. Structure 2008 16, 1095-1104DOI: (10.1016/j.str.2008.03.020) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 3 Docking Model of tRNA Superimposed onto mitPheRS (A) Comparison of the overall fold and domain arrangement in the human mitPheRS (blue) and T. thermophilus PheRS (red). T. thermophilus PheRS represented by CAM, B8, and B8∗ (ABD) domains. Structurally homologous catalytic domains of both PheRSs are presented in the same orientation. (B) The position of the tRNAPhe is obtained after superimposing the mitochondrial onto the bacterial catalytic domain (1eiy); “closed conformation.” The ABD is colored pale green, and the tRNA is colored red. (C) This figure demonstrates that a hinge-type movement (indicated by an arrow) of the mitPheRS C-terminal domain (B8∗-like) would be required to reach the anticodon of tRNAPhe (open conformation). Structure 2008 16, 1095-1104DOI: (10.1016/j.str.2008.03.020) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 4 Recognition of Phenylalanyl-Adenylate (A) Electron density map of phenylalanyl-adenylate in complex with human mitPheRS. The electron density map is contoured at 2.0σ. The protein residues participating in direct and water-mediated contacts with phenylalanyl-adenylate are shown. Water molecules are marked by red spheres. (B) Comparison of the active site of human mitochondrial PheRS, and the catalytic active module (CAM) of T. thermophilus (PDB code: 1pys). MitPheRS is colored blue and CAM is colored red. Structure 2008 16, 1095-1104DOI: (10.1016/j.str.2008.03.020) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 5 Isopotential Surface Representation of mitPheRS A solvent-accessible surface representation of mitPheRS, colored according to electrostatic potential (EP) (red for negative and blue for positive) suggests regions involved in interactions with the negatively charged phosphate backbone of the tRNA molecule. (A) “Closed” conformation. (B) “Open” conformation. (C and D) Three-dimensional representation of long-range EP of human mitPheRS calculated at the distance ± 0.01 kT/e. Model of complex with tRNAPhe in “closed” and “open” conformations. Structure 2008 16, 1095-1104DOI: (10.1016/j.str.2008.03.020) Copyright © 2008 Elsevier Ltd Terms and Conditions