Aminoacyl-tRNA synthetases classes

Figure 29.14. Classes of Aminoacyl-tRNA Synthetases. Class I and class II synthetases recognize different faces of the tRNA molecule. The CCA arm of tRNA adopts different conformations in complexes with the two classes of synthetase.

The close connection of this enzyme family with the transfer of genetic information has made it a popular object of study when dealing with questions regarding the formation and evolution of the genetic code (see Sect. 8.1). It is now agreed that the aminoacyl-tRNA synthetases are a very ancient enzyme species which do not, however, arise from one single primeval enzyme, but from at least two, corresponding to the synthetase classes. 

An important factor in the evolution of the genetic code is certainly provided by the aminoacyl-tRNA synthetases (see Sect. 5.3.2). It is clear that the two synthetase classes are not randomly distributed across the matrix of the amino acid assignment of the genetic code. For example, with one exception, all XUX codons code for class 1 synthetases, while all XCX codons code for class 2 aminoacyl-tRNA synthetases. A possible explanation could be that the synthetases and the genetic code evolved simultaneously. However, it is more likely that these enzymes evolved when the genetic code had already been established (Wetzel, 1995). 

The structures of all the aminoacyl-tRNA synthetases of E. coli have been determined. Researchers have divided them into two classes (Table 27-7) based on substantial differences in primary and tertiary structure and in reaction mechanism (Fig. 27-14) these two classes are the same in all organisms. There is no evidence for a common ancestor, and the biological, chemical, or evolutionary reasons for two enzyme classes for essentially identical processes remain obscure. 

MECHANISM FIGURE 27-14 Aminoacylation of tRNA by aminoacyl-tRNA synthetases. Step is formation of an aminoacyl adenylate, which remains bound to the active site. In the second step the aminoacyl group is transferred to the tRNA. The mechanism of this step is somewhat different for the two classes of aminoacyl-tRNA synthetases (see Table 27-7). For class I enzymes, (2a) the aminoacyl group is transferred initially to the 2 -hydroxyl group of the 3 -terminal A residue, then (3a) to the 3 -hydroxyl group by a transesterification reaction. For class II enzymes, ( the... 

Class II aminoacyl-tRNA synthetases contain a different set of three "signature sequences," two of which form an ATP-binding catalytic domain. The active site structure is built on an antiparallel (3 sheet and is surrounded by two helices (Fig. 29-9). Each class contains subgroups with inserted loops that form other domains. In the following tabulation the reference numbers refer to three-dimensional structural studies. 

Each synthetase module contains three active site domains The A domain catalyzes activation of the amino acid (or hydroxyacid) by formation of an aminoacyl- or hydroxyacyl-adenylate, just as occurs with aminoacyl-tRNA synthetases. However, in three-dimensional structure the A domains do not resemble either of the classes of aminoacyl-tRNA synthetases but are similar to luciferyl adenylate (Eq. 23-46) and acyl-CoA synthetases.11 The T-domain or peptidyl carrier protein domain resembles the acyl carrier domains of fatty acid and polyketide synthetases in containing bound phos-phopantetheine (Fig. 14-1). Its -SH group, like the CCA-terminal ribosyl -OH group of a tRNA, displaces AMP, transferring the activated amino acid or hydroxy acid to the thiol sulfur of phosphopan-tetheine. The C-domain catalyzes condensation (peptidyl transfer). The first or initiation module lacks a C-domain, and the final termination module contains an extra termination domain. The process parallels that outlined in Fig. 21-11.1... 

Comprehensive Biological Catalysis—a Mechanistic Reference Volume has recently been published. The fiiU contents list (approximate number of references in parentheses) is as follows S-adenosylmethionine-dependent methyltransferases (110) prenyl transfer and the enzymes of terpenoid and steroid biosynthesis (330) glycosyl transfer (800) mechanism of folate-requiring enzymes in one-carbon metabohsm (260) hydride and alkyl group shifts in the reactions of aldehydes and ketones (150) phosphoenolpyruvate as an electrophile carboxyvinyl transfer reactions (140) physical organic chemistry of acyl transfer reactions (220) catalytic mechanisms of the aspartic proteinases (90) the serine proteinases (135) cysteine proteinases (350) zinc proteinases (200) esterases and lipases (160) reactions of carbon at the carbon dioxide level of oxidation (390) transfer of the POj group (230) phosphate diesterases and triesterases (160) ribozymes (70) catalysis of tRNA aminoacylation by class I and class II aminoacyl-tRNA synthetases (220) thio-disulfide exchange of divalent sulfirr (150) and sulfotransferases (50). 

Evolutionary relationship of recombinases and topoisomerases Section 27.5.2 Similarities in transcriptional machinery between archaea and eukaryotes Section 28.2.4 Evolution of spliceosome-catalyzed splicing Section 28.2.4 Classes of aminoacyl-tRNA synthetases Section 29.2.5 Composition of the primordal ribosome Section 29,3.1... 

Aminoacyl-tRNA Synthetases Can Be Divided into Two Classes... 

Structural Insights, Aminoacyl-tRNA Synthetases. The first parts of the tutorial focus on the structural differences that distinguish class I and class II aminoacyl-tRNA synthetases. The final section of the tutorial looks at the editing process that most tRNA synthetases use to correct tRNA acylation errors. 

At least one aminoacyl-tRNA synthetase exists for each amino acid. The diverse sizes, subunit composition, and sequences of these enzymes vv ere be vildering for many years. Could it be that essentially all synthetases evolved independently The determination of the three-dimensional structures of several synthetases follo ved by more-refined sequence comparisons revealed that different synthetases are, in fact, related. Specifically, synthetases fall into tvv o classes, termed class I and class II, each of vv hich includes enzymes specific for 10 of the 20 amino acids (Table 29.2). Glutaminyl-tRNA synthetase is a representative of class I. The activation domain for class I has a Rossmann fold (Section 16.1.101. Threonyl-tRNA synthetase (see Figure 29.11) is a representative of class II. The activation domain for class II consists largely of P strands. Intriguingly, synthetases from the tvv o classes bind to different faces of the tRNA molecule (Figure 29.14). The CCA arm of tRNA adopts different conformations to accommodate these interactions the arm is in the helical conformation observed for free tRNA (see Figures 29.5 and 29.6) for class II enzymes and in a hairpin conformation for class I enzymes. These two classes also differ in other ways. 

Why did two distinct classes of aminoacyl-tRNA synthetases evolve The observation that the two classes bind to distinct faces of tRNA suggests at least two possibilities. First, recognition sites on both faces of tRNA may have been required to allow the recognition of 20 different tRNAs. Second, it appears possible that, in some cases, a class I enzyme and a class II enzyme can bind to a tRNA molecule simultaneously without colliding with each other. In this way, enzymes from the two classes could work together to modify specific tRNA molecules. 

P.J. Beuning and K. Musier-Forsyth. 2000. Hydrolytic editing by a class II aminoacyl-tRNA synthetase Proc. Natl. 

Little is known about archaeal aminoacyl-tRNA synthetases, except that the phenylalanyl tRNA synthetases from the archaea Methanosarcina barkeri and S. acidocaldarius resemble their bacterial and eucaryal counterparts in being tetrameric proteins with an aggregate mass of 270 kDda. The archaeal enzymes, however, do not share antigenic determinants with the bacterial and eucaryal enzymes and are functionally restricted to tRNAs of their own lineage [13,14], Thus, they appear to constitute a third class of tRNA charging enzymes, evolutionarily distinct from those of the other domains. 

Classes of aminoacyl-tRNA synthetases. Notice that class I and class II synthetases recognize different faces of the tRNA molecule. 

The answer is c. (Murray, pp 452-467. Scriver, pp 3-45. Sack, pp 1-40. Wilson, pp 101—120.) ATP is required for the esterification of amino acids to their corresponding tRNAs. This reaction is catalyzed by the class of enzymes known as aminoacyl-tRNA synthetases. Each one of these enzymes is specific for one tRNA and its corresponding amino acid. 

E. coli has 20 aminoacyl-tRNA synthetases, each of which recognizes one particular amino acid and one or more tRNAs. There are two general classes of aminoacyl-tRNA synthetases (I and II). They differ in amino acid sequence, the ways in which they bind their cognate tRNAs, and in their quaternary structures. 

How is the proper tRNA recognized by the aminoacyl-tRNA synthetase Interestingly, the anticodon can be all of, part of, or no part of the recognition site for the enzyme. As a result, other regions of the tRNA besides the anticodon must be involved in identifying a tRNA. Figure 27.11 shows the identity elements known for class I and class II tRNAs. 

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