Pseudouridine structure

The base sequence and the tertiary structure of the yeast tRNA specific for phenylalanine (tRNA " ) is typical of all tRNAs. The molecule (see also p.86) contains a high proportion of unusual and modified components (shaded in dark green in Fig. 1). These include pseudouridine (T), dihydrouridine (D), thymidine (T), which otherwise only occurs in DNA, and many methylated nucleotides such as 7-methylguanidine (m G) and—in the anticodon—2 -0-methylguanidine (m G). Numerous base pairs, sometimes deviating from the usual pattern, stabilize the molecule s conformation (2). 

Figure 28-10 Sequence of an E. coli tyrosine tRNA precursor drawn in a hypothetical secondary structure. Nucleotides found modified in the mature tRNA are indicated with their modifications (S4, 4-thiouridine Gm, 2 -0-methylgua-nosine 1°, N6-isopentenyladenosine jt, pseudouridine T, ribothymidine see also Fig. 5-33).241 A partial sequence of the tRNA gene past the CCA end is also shown. Note the region of local 2-fold rotational symmetry (indicated by the bars and the dot). The anticodon 3 -CUA (shaded) of this suppressor tRNA pairs with termination codon 5 -UAG.

The sequences of all three pieces of RNA in the E. coli ribosomes are known as are those from many other species. These include eukaryotic mitochondrial, plas-tid, and cytosolic rRNA. From the sequences alone, it was clear that these long molecules could fold into a complex series of hairpin loops resembling those in tRNA. For example, the 16S rRNA of E. coli can fold as in Fig. 29-2A and eukaryotic 18S RNA in a similar way (Fig. 29-4).38/39/67 69 The actual secondary structures of 16S and 18S RNAs, within the folded molecules revealed by X-ray crystallography, are very similar to that shown in Fig. 29-2A. Ribosomal RNAs undergo many posttranscriptional alterations. Methylation of 2 -hydroxyls and of the nucleic acid bases as well as conversion to pseudouridines (pp. 1638-1641) predominate over 200 modifications, principally in functionally important locations that have been found in human rRNA.69a... 

The C-glycosyl nucleoside antibiotic showdomycin (38) was first isolated from Streptomyces showdoensis [72]. Its structure has striking similarity to uridine (39) and pseudouridine (40), but is distinguished by exhibiting a maleimide moiety (Fig. 19). The known high electrophilicity of this group towards S -nucleophiles... 

Unlike the (3-lactones and (3-lactams, the mode of action of the unusual C-glucosyl nucleoside-based natural product showdomycin is unknown. Nevertheless, this compound has been shown to possess potent antibiotic properties, with results obtained in vitro suggesting a role as a suicide inhibitor of uridine metabolism [11]. Isolated from the bacteria Streptomyces showdoensis, showdomycin contains an electrophilic moiety, malaimide, in place of the base (cf. the structures of uridine or pseudouridine). 

Transfer RNA (tRNA) has the lowest molecular weight, that is, near 28,000. Its function is to activate amino acids for protein biosynthesis. It has a unique cloverleaf structure (Figure 10.29), and there are sections of double-helix, bulges, and hairpin turns. Of all RNAs, it has the highest number of unusual bases (10-15%). Thus, the hairpin arm pointing east contains pseudouridine W and is... 

Transfer RNA (Mr s= 25,000) functions as an adapter in polypeptide chain synthesis. It comprises 10-20 percent of the total RNA in a cell, and there is at least one type of tRNA for each type of amino acid. Transfer RNAs are unique in that they contain a relatively high proportion of nucleosides of unusual structure (e.g., pseudouridine, inosine, and 2 -0-methylnucleosides) and many types of modified bases (e.g., methylated or acetylated adenine, cytosine, guanine, and uracil). As examples, the structures of pseudouridine and inosine are shown below. Inosine has an important role in codon-anticodon pairing (Chap. 17). 

Cyclic Trimer Configuration. The a-cytidine [ACYTID] crystal structure contains two cyclic trimer configurations (Fig. 17.32). In one, N(H)H is engaged in a three-center bond, the other is a homodromic cycle stabilized by a- and w-cooperativity. A comparable situation is found in the crystal structure of a-pseudouridine monohydrate [APSURD] (Fig. 17.13). The glycosyl link is to uracil C(6) instead of N(l), and therefore the N(1)H group is free to donate a hydrogen bond in a homodromic cycle. 

The crystal structure of a-pseudouridine monohydrate [APSURD] (Fig. 17.13) has a particularly strong hydrogen-bond system consisting of a three-bond homo-dromic cycle stabilized by it- and o-cooperativity (see Fig. 17.9b) linked to an infinite chain through the water molecule. 

Figure 5 Structural features of the tRNA from E. coli. Elements involved in recognition by seryl-tRNA synthetase are shaded, antideterminants against recognition by EF-Tu are hatched. The modified bases are D dihydrouridine F pseudouridine i A isopentenyl-adenosine T ribothymidine. Tertiary interactions involving base pairing are indicated by lines, those with intercalations by arrows...

Meroueh M, Grohar PJ, Qiu J, SantaLucia J Jr, Scaringe SA, Chow CS. Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA. Nucleic Acids Res. 2000 28 2075-2083. 

Two structures incorporating modified nucleotides include the co-crystal structure of pseudouridine synthase TruB with a T stem-loop of tRNA in which the modification site (U55) is modified with 5-fluorouridine, " and the crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to DNA containing an abasic site. " ... 

Figure 3-12. The cloverleaf structure of tRNA. Bases that commonly occur in a particular position are indicated by letters. Base-pairing in stem regions is indicated by lines between strands, xy = pseudouridine T = ribothymi-dine D = dihydrouridine.

Figure 30.2 Alanyl-tRNA sequence. The base sequence of yeast alanyl-tRNA and the deduced cloverleaf secondary structure are shown. Modified nucleosides are abbreviated as follows methylinosine (ml), dihydroLindine (UHj). ribothymidine (T), pseudouridine methylguanosine (mG), and diniethylguanosine (m G. Inosine (l. another modified nucleoside, is part of the anticodon.

Figure 4.1 depicts the cloverleaf structure of a tRNA the bars represent base pairs in the stems. There are four arms and three loops - the acceptor, D, T pseudouridine C, and anticodon arms, and D, T pseudouridine C, and anticodon loops. Sometimes tRNA molecules have an extra or variable loop (shown in yellow in Fig. 4.1). The synthesis of transfer RNA proceeds in two steps. The body of the tRNA is transcribed from a tRNA gene. The acceptor stem is the same for all tRNA molecules and added after the synthesis of the main body. It is replaced often during lifetime of a tRNA molecule. The 3-D structure of a yeast tRNA molecule, which can code for the amino acid serine, shows how the molecule is folded with the...

Transfer RNA (tRNA) molecules transport amino acids to ribosomes for assembly into proteins. Comprising about 15% of cellular RNA the average length of a tRNA molecule is 75 nucleotides. Because each tRNA molecule becomes bound to a specific amino acid, cells possess at least one type of tRNA for each of the 20 amino acids commonly found in protein. The three-dimensional structure of tRNA molecules, which resembles a warped cloverleaf (Figure 17.22), results primarily from extensive intrachain base pairing. tRNA molecules contain a variety of modified bases. Examples include pseudouridine, 4-thiouridine, 1-methylguanosine, and dihydrouridine ... 

The term C-nucleoside was only coined after isolation and characterization of the first member of this class pseudouridine, in 1975 [97ACH(ip)]. Before that, alditolyl derivatives of some heterocycles (acyclo C-nucleo-sides) were known both as natural products (alditolyl pteridines or biopterins) as well as products of syntheses (e.g., alditolyl derivatives of imidazoles, benzimidazoles, thiazoles, benzothiazoles, 1,2,3-triazoles, quinoxalines, and flavazoles) and were classified as carbohydrate derivatives of heterocyclic compounds. After isolation of pseudouridine, other naturally occurring members were successively isolated, characterized, and synthesized. It is worth mentioning that synthesis preceded isolation in two cases 9-dea-zaadenosine and pyrrolosine. Comparison with the synthetic compounds facilitated structure elucidation in one case (9-deazaadenosine) and structure reassignment in the other (pyrrolosine). 

The pseudouridines within the H69 loop are synthesized by the RulD protein, one of the few modification enzymes in E. coli that is required for normal growth, that is, the mutant is severely impaired. Consistent with the findings of Noller and coworkers, and the modification results of Maivali and Remme, biochemical evidence supports a role for pseudouridine modification where a specific -dependent structure of H69 is necessary for subunit association. Our current understanding of the ribosome structure is insufficient to ascertain whether the ips are directly involved in subunit interactions, or whether modification causes a conformation change involving other conserved bases in the H69 loop. Since "0 modification of H69 is absolutely conserved and necessary for proper function, an understanding of the influence of modification on structure would be informative. 

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