Aminoacyl-tRNA synthetases, domains

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. 

Many proteins have structures related to those of aminoacyl-tRNA synthetases.282 283 For example, asparagine synthetase A functions via an aspartyl-adenylate intermediate (Chapter 24, Section B), and its structure resembls that of aspartyl-tRNA synthetase.284 The his G gene of histidine biosynthesis (Fig. 25-13) encodes an ATP phosphoribosyltransferase with structural homology to the catalytic domain of histidyl-tRNA synthetase.284 The reason is not clear, but some aminoacyl-tRNA synthetases, especially the histidyl-tRNA synthetase, are common autoantigens for the inflammatory disease polymyosititis.285 286... 

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... 

Norcum MT, Warrington JA. Structural analysis of the multienzyme aminoacyl-tRNA synthetase complex A three domain model based on reversible chemical cross-linking. Protein Sci 1998 7 79-87. 

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. 

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. 

Alexander, R. W., and P. Schimmel. 2001. Domain-domain communication in aminoacyl-tRNA synthetases. Prog. Nucieic Acid Res. Mol Biol 69 317-349. 

Aravind L, Anantharaman V, Koonin EV Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains Implications for protein evolution in the RNA world. Proteins-Structure Function and Genetics 2002, 48(1) 1-14. 

FIGURE 4 Domain organization of synthetases and tRNAs. The class-defining domain of the aminoacyl-tRNA synthetase contains conserved structural features and contacts the acceptor arm of tRNA. These contacts are mediated by additions to the classdefining catalytic domain. Appended nonconserved protein domains interact with other portions of the tRNA, including in many cases the anticodon (as indicated by the dotted line). [From Schim-mel, R, and Ribas de Pouplana, L. (1995). Cell81, 983-986.]... 

Figure 29-9 Selected views of aminoacyl-tRNA sjmthetase stmcture and action. (A) Alpha-carbon trace of the type IE. coli glutaminyl-tRNA synthetase. The phosphate backbone of tRNA " is shown in black ATP is shown in the active-site cleft. The canonical dinucleotide fold domain near the N terminus is shaded. Two structural motifs (black), proposed to link the active site with regions of the protein-RNA interface involved in tRNA discrimination, are indicated. The a helix (top) connects tRNA recognition in the minor groove of the acceptor stem with binding of the ribose group of ATP. The large loop (center) connects anticodon recognition by the two P-barrel domains (bottom) with sequences flanking the MSK sequence motif, which interacts with the phosphates of ATP. From Perona et Courtesy of Thomas A. Steitz. (B) The active site...

Nonribosomal peptide synthesis means that the peptide is not produced by the tRNA-mRNA mechanism described in Chapter 28, Section 28.6. Each amino acid found in 224 is directly selected for incorporation into the growing peptide chain by one of the domains of surfactin synthetase, shown with the pendant SH groups. Substrate activation occurs after binding the amino acid, and the enzyme catalyzes the formation of an aminoacyl adenylate intermediate using Mg2+-ATP and release of a cofactor. Subsequently, the amino acid-O-AMP oxoester is converted into a thioester by a nucleophilic attack of the free thiol-bound cofactor of an adjacent PCP domain. (Note that ATP is adenosine triphosphate and AMP is adenosine monophosphate see Chapter 28, Section 28.5.)... 

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