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. 2000 May 15;19(10):2351–2361. doi: 10.1093/emboj/19.10.2351

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graphic file with name cdd233f1a.jpg — Fig. 1. (A) Stereo ribbon diagram of the structure of the complex between T.thermophilus leucyl-tRNA synthetase and a leucyl-adenylate analogue. The domains are coloured as follows: N-terminal extension (pale green), catalytic domain (Rossmann-fold, orange), ZN-1 domain (blue), helical hairpin insertion (green), editing domain (cyan), ZN-2 domain (yellow), leucyl-specific insertion domain (black), connecting module (purple), anti-codon binding domain (red) and C-terminal extension (pink). The zinc atoms are shown as red balls and the leucyl-adenylate analogue as a space-filling model in the centre. The N- and C-termini are marked. (B) Stereo ribbon diagram of the structure of the T.thermophilus isoleucyl-tRNA synthetase. Colouring as in (A). Note that in IleRS the ZN-1 domain is split by the inserted editing domain [see (C) and Figure 2]. (C) Comparison of point of insertion of extra domains in T.thermophilus leucyl- (top) and isoleucyl- (bottom) tRNA synthetases. For clarity, the enzymes are C-terminally truncated just before the anti-codon binding domain (C′). The purple polypeptide segment is homologous in each enzyme and contains the second half of the ZN-1 binding site [see also (A)]. In leucyl-tRNA synthetase, it precedes the editing domain (cyan), whereas in isoleucyl-tRNA synthetase it follows the editing domain (green). The disposition of the leucyl-specific insertion domain is shown in black. It is inserted just before the KMSKS loop (red segment in both enzymes). (D) Stereo view of the superposition of C_α traces of LeuRSTT and IleRSTT showing different points of insertion of the editing domain and the near 180° difference in rotational orientation. LeuRSTT is red with editing domain cyan, leucine-specific domain black and LeuAMS in the active site. IleRSTT is yellow with editing domain green. Considering the red and yellow traces, 437 C_α positions superpose within a cut-off of 3.8 Å with 115 identities and root-mean-square deviation (r.m.s.d.) of 1.99 Å. Superposing the two editing domains, the equivalent figures are 129 C_α positions with 37 identities and r.m.s.d. of 1.36 Å. In all, 69.5% of the 814 ordered residues in LeuRSTT can be superposed within 3.8 Å of equivalent residues in IleRSTT with 27% of these residues being identical.

graphic file with name cdd233f1b.jpg — Fig. 1. (A) Stereo ribbon diagram of the structure of the complex between T.thermophilus leucyl-tRNA synthetase and a leucyl-adenylate analogue. The domains are coloured as follows: N-terminal extension (pale green), catalytic domain (Rossmann-fold, orange), ZN-1 domain (blue), helical hairpin insertion (green), editing domain (cyan), ZN-2 domain (yellow), leucyl-specific insertion domain (black), connecting module (purple), anti-codon binding domain (red) and C-terminal extension (pink). The zinc atoms are shown as red balls and the leucyl-adenylate analogue as a space-filling model in the centre. The N- and C-termini are marked. (B) Stereo ribbon diagram of the structure of the T.thermophilus isoleucyl-tRNA synthetase. Colouring as in (A). Note that in IleRS the ZN-1 domain is split by the inserted editing domain [see (C) and Figure 2]. (C) Comparison of point of insertion of extra domains in T.thermophilus leucyl- (top) and isoleucyl- (bottom) tRNA synthetases. For clarity, the enzymes are C-terminally truncated just before the anti-codon binding domain (C′). The purple polypeptide segment is homologous in each enzyme and contains the second half of the ZN-1 binding site [see also (A)]. In leucyl-tRNA synthetase, it precedes the editing domain (cyan), whereas in isoleucyl-tRNA synthetase it follows the editing domain (green). The disposition of the leucyl-specific insertion domain is shown in black. It is inserted just before the KMSKS loop (red segment in both enzymes). (D) Stereo view of the superposition of C_α traces of LeuRSTT and IleRSTT showing different points of insertion of the editing domain and the near 180° difference in rotational orientation. LeuRSTT is red with editing domain cyan, leucine-specific domain black and LeuAMS in the active site. IleRSTT is yellow with editing domain green. Considering the red and yellow traces, 437 C_α positions superpose within a cut-off of 3.8 Å with 115 identities and root-mean-square deviation (r.m.s.d.) of 1.99 Å. Superposing the two editing domains, the equivalent figures are 129 C_α positions with 37 identities and r.m.s.d. of 1.36 Å. In all, 69.5% of the 814 ordered residues in LeuRSTT can be superposed within 3.8 Å of equivalent residues in IleRSTT with 27% of these residues being identical.