Acceptor arm

All tRNA molecules contain four main arms. The acceptor arm terminates in the nucleotides CpCpAoH. These three nucleotides are added posttranscription-ally. The tRNA-appropriate amino acid is attached to the 3 -OH group of the A moiety of the acceptor arm. 

The regions of the tRNA molecule teferred to in Chapter 35 (and illustrated in Figure 35-11) now become important. The thymidine-pseudouridine-cyti-dine (T PC) arm is involved in binding of the amino-acyl-tRNA to the ribosomal surface at the site of protein synthesis. The D arm is one of the sites important for the proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase. The acceptor arm, located at the 3 -hydroxyl adenosyl terminal, is the site of attachment of the specific amino acid. 

All tRNAs in solution fold into a three-dimensional L-shaped structure like that of tRNAphe (fig. 29.5b). This structure is composed of two helical arms joined at right angles. The ribose moiety to which the amino acid is joined is at the end of one arm, identifying it as the acceptor arm. The anticodon is at the end of the other arm, identifying it as... 

Regarding the stmctural features that enable EF-Tu and SelB to distinguish their tRNAs, an extensive mutational analysis was performed and synthetic RNA minihelices were analyzed for binding to EF-Tu and SelB. It was found that both the length of the aminoacyl-tRNA acceptor stem and the basal helical part of the acceptor arm were crucial. ... 

All tRNAs have a similar three-dimensional structure that includes an acceptor arm for attachment of a specific amino acid and a stem-loop with a three-base anticodon sequence at its ends (see Figure 4-22). The anticodon can base-pair with its corresponding codon in mRNA. 

Cooperativity/competUion among acceptors (armed/disarmed carbohydrates) Cleavage of the C-X bond at the anomeric position proceeds via evolution of the anomeric n o C-X interaction that culminates in the oxocarbenium ion. This carbocation is so strongly stabilized by n j- p interaction that this interaction is commonly described as a dative it-bond. Because oxacarbenium ions are strongly stabilized, their formation is relatively facile. In cross-coupling glycosylalion reactions, however, it is beneficial to differentiate the reactivity of two saccharides for the selectivity reasons. The competition and cooperativity between stereoelectronic effects can be used to fine-tune the reactivity of anomeric systems. 

Uij = Rij/Rij. Similarly, Ga[(ljp u /) + 1] attains its maximum value whenever the direction of the acceptor arm Ij is in the direction -u//. Thus, the product of these three functions attains a value close to unity only if, simultaneously, Rij is about Rh, the direction of Hia is about that of Xij, and the direction of jp is about that of -u /. Such a configuration is said to be favorable for HB formation. Clearly, if all of the above three conditions are fulfilled, then the interaction energy is about sub- The sum of the various terms in the curly brackets of (2.7.8) arises from the total of eight possible favorable directions for HB formation (four when molecule i is a donor and four when molecule i is an acceptor). The variances a and a are considered as adjustable parameters. Note that of the eight terms in the curly brackets, only one may be appreciably different from zero at any given configuration X Xy. Clearly, the HB part of the potential in (2.7.8) does not suffer from a possible divergence as in the Bjerrum model, and clearly does not allow two bonds to be formed by a pair of water molecules (Fig. 2.48b). 

Note also that in Eq. (2.7.8) we accounted only for configurations that are favorable for HBing. In a more realistic function, one might add another eight terms to (2.7.8) to account for the electrostatic repulsion whenever two donors or two acceptor arms approach each other. In some of our order-of-magnitude estimates presented in this and in the next chapter, we shall not need any detailed description of the potential function, and we can also ignore the distinction between a donor and an acceptor arm. 

The second term on the right-hand side of (2.7.47) is the conditional solvation Helmholtz energy for the process of turning on the four arms of the water molecule. Strictly, we have to distinguish between the two donor arms and the two acceptor arms (Sec. 2.7.2). However, for all our purposes we can disregard this distinction and assume that this term is simply four times the conditional solvation Helmholtz energy of one arm, which we designate as the arm a. Hence, we write... 

To what extent is this assumption justified To answer this question, we analyze the quantity on the Ihs of (B.l) using an argument similar to the one used in section 7.7. For notational simplicity, we assume that all arms are equivalent (the same conclusion applies when we distinguish between the donor and acceptor arms) ... 

One of the four arms of the tRNA secondary structure is the acceptor arm. It consists of seven base pairs and a single-stranded 3 -terminus. At the 3 -terminal nucleotide (invariably A76), the amino acid is specifically attached. The aminoacylation of the tRNA occurs by esterification of the amino acid to the 2 or 3 -OH group of the ribose of adenosine A76 [15]. This reaction is catalyzed by aminoacyl-tRNA synthetases. 

Earlier biochemical studies have demonstrated that in many cases the main identification features or recognition elements necessary for the correct recognition of tRNAs by their cognate aminoacyl-tRNA synthetases are localized in the acceptor stem [16-19]. Frequently, these recognition sites are referred to as identity elements since they make this particular tRNA unique and distinguishable from all other tRNAs for the corresponding aminoacyl-tRNA synthetase. For the tRNA from E. coli it could be shown by the groups of Schim-mel [20, 21] and McClain [19, 22-24] that a wobble base pair G3-U70 at position 3 of the acceptor arm represents the major identity element. 

Subsequently, it was demonstrated that even a truncated tRNA, consisting only of the acceptor arm with the single-stranded 3 -end, is recognized as a substrate by the alanyl-tRNA synthetase (ARS) and correctly aminoacylated with alanine [21, 25], provided that the G3-U70 base pair is present at the correct location. 

Figure 19.4 Imino region of the H NMR spectra of the acceptor arm duplex derived from yeast tRNA ° before (lower trace) and after (upper trace) addition of 7.5 pM MnCl2 (RNA concentration 1.65 mM, 7.5 mM MgCy at 277 K.

Though one-dimensional H NMR studies of the tRNA acceptor arm gave hints to the special role of the G-U base pair, detailed information on the possible modifications of the local helical geometry in the vicinity of the G-U pair caimot be obtained by these experiments. 

Figure 19.5 Schematic representation of the observed intemucleotide NOESY contacts in the E. coli tRNA derived acceptor arm duplex (18mer/GU) for mixing time of 300 ms at 303 K.

Figure 19.7 Model of the tRNA acceptor arm structure as determined on the basis of the 300 ms NOESY spectrum using the IRMA procedure [45] and restrained molecular dynamics. Three structures resulting from different calculations are superimposed. The continuation of the helix geometry into the single-stranded terminus is clearly visible. The black sphere marks the most probable location of the bound manganese ion in the vicinity of G3-U70 base pair.

The results presented above demonstrate that there is a deviation from the regular A-hehcal geometry in the wild-type tRNA acceptor arm that is mainly characterized by a displacement of the U70 base. Thereby the base plane overlap between C71 and U70 is dis-... 

The two portions of the L can be considered distinct domains with separate contributions to protein synthesis. The minihelix containing the acceptor arm includes the site of amino acid attachment (the 3 -OH). It is considered by many investigators to be related to the historical or early form of tRNA. The anticodon trinucleotide is located at the other end of the L, approximately 75 A away. This... 

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