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Chapter 20 : The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase

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Abstract:

This chapter reviews the recognition specificity of a class II aminoacyl-tRNA synthetases (aaRS) and AspRS in detail. Class II aaRS are characterized by three signature motifs, each containing strictly conserved residues. The crystal structures of SerRS from and AspRS from yeast gave a clear structural explanation for the partition into the two classes. Indeed, class II aaRS contain a new fold, consisting of an antiparallel β sheet flanked by two α helices. The structures of the complex formed by tRNA and AspRS from yeast, with or without ATP correlate these motifs with their biological function; highly conserved residues from motifs 2 and 3 are responsible for ATP binding. Seven class II aaRS exhibit motifs 1 , 2 , and 3. More stringent sequence homology requirements led to the definition of subclasses. Class IIc aaRS (GlyRS, AlaRS, and PheRS) do not contain motif 1 and have a different quaternary organization. PheRS is an even more special case because it has the motif 2 and 3 characteristics of class II but behaves like a class I synthetase as to its primary site of aminoacylation.

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20

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Amino Acids
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Saccharomyces cerevisiae
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Aspartic Acid
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Escherichia coli
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Figures

Image of Figure 1.
Figure 1.

Alignment of aspartyl-tRNA synthetase sequences of different origins. The following abbreviations are used for mitochondria: Ysc, yeast cytoplasm; Hum, human; Rat, rat liver; See, ; Eco, ; Tth, ; Smt, mitochondria. Residues invariant in all synthetases are in boldface. The location of residues involved in tRNA and aspartic acid binding are shown above the sequence, and the location of residues involved in ATP binding as well as the three motifs of class II aaRS are shown below the sequence. The secondary structure elements for yeast AspRS are shown above the sequence with the same convention used in Fig. 2 (S, strand; H, helix).

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
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Image of Figure 2.
Figure 2.

Yeast AspRS structure: overall structure (A), N-terminal domain (B), active site (C). Black and white figures were produced using the program Molscript, written by Kraulis ( ).

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
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References

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Tables

Generic image for table
Table 1.

Classification of aminoacyl-tRNA synthetases

Aminoacyl tRNA synthetases charge their amino acid to the 2′-OH (class I) or the 3′-OH (class II) of the ribose of the terminal adenosine. The ATP binding site is different for the two classes.

The aaRS does not recognize the anticodon.

The aaRS structure has been determined in at least one species.

The aaRS needs the tRNA for aminoacyladenylate formation.

Motifs 2 and 3 only.

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
Generic image for table
Table 2.

Homology and identity in AspRS

Ysc, yeast cytoplasmic; Hum, human; Rat, rat liver; See; Eco, ; Tth, ; Smt, mitochondrial.

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20
Generic image for table
Table 3.

Crystallographic data for the AspRS system

The solvent content values given here assume an average density of the crystals of 1.15 g/cm. The molecular masses used are as follows: yeast AspRS (62.5 kDa per monomer, 557 residues); AspRS (66 kDa per monomer, 591 residues); AspRS (66 kDa per monomer, 580 residues); yeast tRNA (24,160 Da, 75 nucleotides); tRNA (25,000 Da, 77 nucleotides).

Citation: Cavarelli J, Moras D. 1995. The Aspartic Acid tRNA System: Recognition by a Class II Aminoacyl-tRNA Synthetase, p 411-422. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch20

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