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Color Plates

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Figures

Image of Color plate 1

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Color plate 1

Difference of thermal mobility distribution for tRNA (left) and tRNA (right) as revealed by use of color coding (see reference 45 in chapter 8). Pure blue and pure red are associated with, respectively, the least and most mobile part within each molecule. The CCA-end of each molecule has been left blank to show that they were not considered for the determination of the color code of the residues because the CCA-end conformation of the tRNA molecule could not be determined. Its conformation in this figure is a standard helical conformation.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 2

Comparison of computer-predicted nucleotide determinants of tRNA acceptor identity with those observed experimentally. The tRNA chain is in blue, and each nucleotide position is a yellow circle whose diameter is proportional to the fraction of the 20 tRNA acceptor types for which the nucleotide position was a predicted or observed determinant. Reproduced from reference 37 and 46 in chapter 16, with permission.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 3

Positions and regions of GlnRS that are important for tRNA specificity. The residues identified by genetic, biochemical, and biophysical studies are marked on a ribbon diagram of the crystal structure of the complex of GlnRS:tRNA (see reference 75 in chapter 19). Mutations in these regions of GlnRS lead to relaxed specificity with respect to noncognate tRNAs and/or mutant cognate tRNAs. Labeled with capital letters are the approximate positions of Ilel29 (I), Leul36 (L), Asp235 (D), Prol81 (P), and Gln318 (Q). Colored are helix/loop E (blue), loop I (yellow), and helix H (red). (Adapted from references 11, 24, 64, 70 , 74 , 75 , 84, 89 , 95 and 96 in chapter 19.)

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 4

Deletion mutants of E. coli GlnRS(D235N), which retain the ability to mischarge (SuUAG) <in line graphic> in vivo (see reference 82 in chapter 19). The largest deletions tolerated in the accepter binding domain (blue) and the anticodon binding domain (red) are indicated on a ribbon diagram from the crystal structure of the GlnRS:tRNA complex (see reference 75 in chapter 19). Combinding the acceptor and anticodon binding domain deletions gives rise to a “minimal” GlnRS, which still weakly mischarges (SuUAG). D, position of Asp235.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 5

Anticodon recognition and functional and structural connectivity in GlnRS. The anticodon recognition signal must be transmitted to the active site. Colored on this ribbon diagram of the GlnRS:tRNA complex (see reference 75 in chapter 19) are two regions of GlnRS proposed to be involved in connecting the acceptor and anticodon binding domains (red) and the anticodon binding domain and active site (blue) (see references 70, 74, 75 , 95 in chapter 19). Also marked are the approximate positions of residues implicated in anticodon recognition, acceptor stem recognition, and/or functional communication: Arg341 (R), Arg402 (R4), Glu323 (E), Gln318 (Q), Asp235 (D), Prol81 (P), and Leul36 (L) (see references 64, 70 , 74 , 75 , 84, 96 in chapter 19). Finally, the approximate positions of the anticodon bases of tRNA are marked with small letters (c, u, and g) (see reference 75 in chapter 19).

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 6

The close evolutionary relationship between the glutamate and glutamine systems is more clear for the aaRS (left) than for the tRNAs (right). Superimposed on a ribbon diagram of the GlnRS:tRNA complex structure (see reference 74 in chapter 19) are the short conserved amino acid sequences found in all bacterial GluRS. These sequences align with parts of the dinucleotide and acceptor binding domains of GlnRS. Yellow represents conservation, which is unique to GluRS and GlnRS; blue represents general class 1 motifs. Only the mischarging bacterial GluRS's (i.e., those that recognize tRNA) share homology with the anticodon binding domain (red) of GlnRS (see reference 6 in chapter 19). On the other hand, very few of the glutamine recognition elements (boxed and circled positions) are conserved between tRNA and tRNA. Open dots, no homology; filled squares, generally conserved nucleotides; letter of the nucleotide, specific homology between two tRNAs.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 7

tRNA structure: free tRNAA sP crystal, A form (B); tRNA complexed with the protein (A); and superposition of the two tRNAs (C). The superposition has been done at the level of the tertiary interactions. The figure was made by using the program O (see reference 28 in chapter 20).

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 8

Yeast tRNA aspartyl-tRNA synthetase complex. For the monomer (A), the tRNA is shown in stick representation and the ATP molecule is shown in cpk representation. The dimer is shown in panel B. The figure was made by using the program O (see reference 28 in chapter 20) or the program RIBBONS (see reference 7 in chapter 20). The ATP molecules are shown in red with a ball-and-stick representation.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 9

Schematic representation of eukaryotic and prokaryotic AspRS. The figure was made by using the program O (see reference 28 in chapter 20). Motif I is in green, motif 2 is in red, and motif 3 is in yellow.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 10

Structure of AspRS from (see reference 13 in chapter 20). The figure was made by using the program O (see reference 28 in chapter 20).

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 11

ATP (A) and AMPPcP (B) binding sites in yeast AspRS. The figure was made by using the program RIBBONS (see reference 7 in chapter 20). Motif is in red, motif 2 is in green, and motif 3 is in blue.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 12

tRNA-AspRS interactions. The acceptor stem with motif 1 is shown in green, motif 2 is shown in blue, and motif 3 is shown in yellow (A); G10-U25 region (B); and anticodon domain (C). The figure was made by using the program O (see reference 28 in chapter 20) or the program RIBBONS (see reference 7 in chapter 20).

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 13

Three-dimensional model of nicked EFTu: GDP lacking amino acid residues 41 to 59. The four loops defining the GDP binding site are located in the domain I. The figure was generated by using the program Molscript by Kraulis (see reference 53 in chapter 21).

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 14

Tertiary structure model of EF-Tu:GDP NNP from and . The figure was generated by using the program Molscript by Kraulis (see reference 53 in chapter 21).

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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Color plate 15

Regions of tRNAsMet important for specifying various special properties of tRNA highlighted in color in cloverleaf structure. Sites in the tRNA that have been mutagenized are indicated by dots (substitution) or a triangle (deletion). Arrows identify specific mutations that affect significantly the phenotype of the tRNA with respect to a particular function.

Citation: . 1995. Color Plates, In tRNA. ASM Press, Washington, DC.
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