Aminoacyl‐tRNA Synthetases: The Division into Two Classes Predicted by the Chemistry of Substrates and Enzymes

Cramer, Friedrich; Freist, Wolfgang

doi:10.1002/anie.199301901

Cited by 19 publications

(5 citation statements)

References 102 publications

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“…(1) The terms C,,[E,] describe the rates between the segments, and D, [E,] is the sum of the concentrations of the intermediates within the given segment. The rate equations are in Eqns (2)(3)(4).…”

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confidence: 99%

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Airas

1996

European Journal of Biochemistry

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The magnesium dependences of the ATPJPP, exchange and tRNA aminoacylation of reactions were measured for six aminoacyl-tRNA synthetases (isoleucyl-, tyrosyl-and arginyl-tRNA synthetases from class I, and histidyl-, lysyl-and phenylalanyl-tRNA synthetases from class 11). The measured values were subjected to best-fit analyses using sum square error calculations between the data and the calculated curves in order to find the mode of participation of the Mg" and to optimize the sets of the kinetic constants.The following four dependences were observed: the class I1 synthetases require three Mgz+ for the activation reaction (including the one in MgATP), but the class I synthetases require only one Mgz+ (in MgATP) ; in class I1 synthetases both MgPP, and Mg,PP, participate in the pyrophosphorolysis of the aminoacyl adenylate. Arginyl-tRNA synthetase from class I also shows a better fit if also Mg,PP, reacts, but in the isoleucyl-and tyrosyl-tRNA synthetases only MgPP, but not Mg,PP, is used in the pyrophosphorolysis. Different synthetases have different requirements for the tRNA-bound Mg2+ and spermidine, independent of the enzyme class. 1-4 Mg" or spermidines are required in the best fit models. At the end of the reaction in all the synthetases analysed the dissociation of Mg" from the product aminoacyltRNA essentially enhances the subsequent dissociation of the aminoacyl-tRNA from the enzyme. The binding of ATP to the E . aminoacyl-tRNA complex also speeds up the dissociation of the aminoacyltRNA from most of these enzymes.

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Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Airas

1996

European Journal of Biochemistry

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“…Studies on substrate specificity with regard to ATP analogues showed that only two of sixteen analogues were substrates for the enzyme from baker's yeast (2-chloro-ATP and formycin triphosphate) whereas six were inhibitors (Freist et al, 1978). Compared with other aminoacyl-tRNA synthetases the enzyme specific for threonine exhibits a substrate specificity with regard to ATP analogues which is typical for class II synthetases (Freist etai, 1981;Cramer and Freist, 1993).…”

Section: Aminoacylation Mechanism and Substrate Specificitymentioning

confidence: 99%

Review

1995

Biological Chemistry Hoppe-Seyler

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One of the salient features of the mammalian genome is the vast excess of DNA without obvious function, such as repetitive DNAs, spacers, and introns. In recent years, microsatellites, which include short triplet repeats (mostly CAGn and CGGn) and dinucleotide repeats (notably CAn) have gained widespread attention, along with minisatellites which consist of somewhat longer repeat units. Micro- and minisatellites, collectively called variable number tandem repeats (VNTRs), can be highly unstable and display an amazing degree of polymorphism. This property is exploited for gene mapping, for tumor diagnosis, and in forensic medicine. Undue expansion of gene-associated microsatellites is also responsible for some severe genetic diseases, such as fragile X syndrome. Most or all of these diseases are caused by expansion of CAG and CGG triplets. Within protein-coding regions these triplets usually code for polymers of glutamine, serine, alanine or proline. Physiologically, such amino acid repeats are often found in transcription factors and can increase or decrease their activity, depending on the repeat number. Alone or in conjunction with DNA methylation, such repeats may offer a unique opportunity for subtle, semi-stable modulation of gene activity. Also, at least in some plants and perhaps other organisms, a quasi-Lamarckian inheritance is mediated by repetitive DNA. Generally, repetitive DNA sequences, whether represented by short or by long DNA segments, may be beneficial for the evolution of a species.

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“…Much attention has been paid to the editing mechanisms, which eliminate the erroneously formed products, pretransfer proofreading at the aa‐AMP level and post‐transfer proofreading at the aa‐tRNA level . The aminoacyl‐tRNA synthetases have been divided into two classes according to structural and functional properties . Isoleucyl‐tRNA synthetase (IleRS) falls into Class Ia together with other synthetases for the branched chain amino acids.…”

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Kinetic analysis of the isoleucyl‐tRNA synthetase mechanism: the next reaction cycle can start before the previous one ends

Airas

2017

FEBS Open Bio

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Aminoacyl‐tRNA synthetases join correct amino acids to their cognate tRNA at the start of the protein synthesis. Through the kinetic analysis, it is possible to estimate how their functional details correspond to the known structural features. Kinetic analysis of the isoleucyl‐tRNA synthetase (IleRS) from Escherichia coli was accomplished. Sixteen different steady‐state two‐ligand experiments were statistically analysed simultaneously so that the same rate equations and same rate and dissociation constants applied to all experiments. The so‐called rapid equilibrium segments procedure was used to derive the rate equations. The final best‐fit mechanism included the normal activation and transfer steps, and reorganization of the steps between them and after the transfer step. In addition, the analysis strongly suggested an additional activation step, formation of a new isoleucyl‐AMP before the isoleucyl‐tRNA was freed from the enzyme. The removal of Ile‐tRNA was possible without the formation of Ile‐AMP if both isoleucine and ATP were bound to the E‐Ile‐tRNA complex, but this route covered only 11% of the total formation of Ile‐tRNA. In addition to the Mg 2+ in MgATP or MgPP i , only two tRNA‐bound Mg 2+ were required to explain the magnesium dependence in the best‐fit mechanism. The first Mg 2+ could be present in all steps before the second activation and was obligatory in the first reorganizing step and transfer step. The second Mg 2+ was present only at the transfer step, whereas elsewhere it prevented the reaction, including the activation reactions. Chloride inhibited the IleRS reaction, while 100 m m KCl caused 50% inhibition if the ionic strength was kept constant with K‐acetate. The (tRNA) value was increased from 0.057 to 1.37 μ m when the KCl concentration was increased from 0 to 200 m m . The total rate equation helps to understand the reaction route and how the simultaneous presence of Ile‐tRNA and Ile‐AMP can cause new possibilities to proofreading mechanisms of this enzyme. Enzyme Isoleucyl‐tRNA synthetase ( EC 6.1.1.5 )

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Aminoacyl‐tRNA Synthetases: The Division into Two Classes Predicted by the Chemistry of Substrates and Enzymes

Cited by 19 publications

References 102 publications

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Review

Kinetic analysis of the isoleucyl‐tRNA synthetase mechanism: the next reaction cycle can start before the previous one ends

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