Transglycosylation: a mechanism for RNA modification (and editing?) - PubMed (original) (raw)

Review

Transglycosylation: a mechanism for RNA modification (and editing?)

George A Garcia et al. Bioorg Chem. 2005 Jun.

Abstract

The vast majority of the ca. 100 chemically distinct modified nucleosides in RNA appear to arise via the chemical transformation of a genetically encoded nucleoside. Two notable exceptions are queuosine and pseudouridine, which are incorporated into tRNA via transglycosylation. Transglycosylation is an extremely efficient process for incorporating highly modified bases such as queuine into RNA. Transglycosylation is also a requisite process for "isomerizing" an N-nucleoside into a C-nucleoside as is the case for pseudouridine formation. Finally, transglycosylation is an attractive possibility for certain RNA editing events (e.g., pyrimidine to purine conversions) that cannot occur via the known, more straightforward enzymatic reactions (e.g., deaminations). This review discusses what is known about the mechanisms of transglycosylation for the queuine and pseudouridine RNA modifications and will speculate about a potential role for transglycosylation in certain RNA editing events.

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Figures

Fig. 1

Structures of guanine, queuine, and archaeine (the base of archaeosine). Note that the N7 of the purine ring system corresponds to the C5 of the pyrrolopyrimidine ring system.

Fig. 2

Queuosine and archaeosine biosynthetic pathways. Archaeosine is found in the D-loop of many archaeal tRNAs. Queuosine occurs in the wobble position of the anticodon of tRNAs (Asp, Asn, His, and Tyr) in both eubacteria and eukarya.

Fig. 3

Active site of Z. mobilis TGT with PreQ1 bound. Aspartates 89 and 264 form a roughly equilateral triangle with N7 (corresponding to the purine N9) of preQ1 with sides ca. 6 Å. (Structure is from coordinates communicated by Dr. Ralf Ficner.)

Fig. 4

Two potential chemical mechanisms for the TGT reaction involving two aspartates. In the “associative mechanism,” an aspartate acts as a nucleophile to displace guanine. In the “dissociative mechanism,” an aspartate stabilizes an oxocarbenium ion intermediate. In both mechanisms, a general acid (either enzymic or water) serves as a proton donor to facilitate the departure of guanine.

Fig. 5

Crystal structure of the covalent complex between the Z. mobilis TGT and RNA. This structure (PDB Accession No. 1Q2R) was generated from crystals of the Z. mobilis TGT complexed with a minihelical RNA and 9-deazaguanine [17]. Aspartate 264 forms a covalent bond with the 1′ position of the ribose corresponding to #34. Guanine 34 has been displaced and 9-deazaguanine is occupying the guanine/preQ1 site.

Fig. 6

Chemical mechanism for the TGT reaction that is consistent with biochemical and structural data. Two active-site aspartate residues serve critical roles in catalysis by TGT. Aspartate 264 nucleophilically attacks the 1′-ribosyl carbon, resulting in a TGT–RNA covalent linkage and the displacement of the guanine base. It is hypothesized that aspartate 89 might be responsible for protonation of the guanine base and/or deprotonation of the incoming preQ1 (perhaps through the intermediacy of water). While guanine is shown being protonated at N7, protonation could be directly at N9.

Fig. 7

Pseudouridine synthase reaction.

Fig. 8

Postulated pseudouridine mechanism involving a cysteine nucelophile. The cysteine thiolate attacks C6 forming a dihydrouridine-like complex. Scission of the glycosidic bond yields an oxocarbenium ion intermediate. Attack of C5 upon the 1′ position following rotation of the uracil reforms the glycosidic bond. Elimination of the enzymic thiolate, followed by tautomerization yields pseudouridine.

Fig. 9

Postulated pseudouridine mechanisms involving an aspartic acid nucleophile. (A) “C6 Attack” or “Michael addition” mechanism. (B) “1′ Attack” or “Acylal” mechanism.

Fig. 10

Consensus sequences around catalytically important aspartic acids in tRNA-guanine transglycosylase and pseudouridine synthase. For those residues that vary somewhat, the variant amino acids are shown in parentheses below the consensus amino acid in the figure.

Fig. 11

Deaminase mechanisms for C to U and A to I editing. An enzymically activated water molecule attacks the base in an addition–elimination mechanism which ultimately replaces the amine with an oxygen (carbonyl).

Fig. 12

Postulated mechanisms for pyrimidine to purine editing. Mechanisms are shown for the U to A conversion. Similar mechanisms are possible for U to G and C to A conversions. (A) “Excision–Ligation” mechanism, where the elements of UMP are excised from the oligonucleotide followed by the insertion and ligation of the elements of AMP. (B) “Transglycosylation” mechanism, where, similar to tRNA-guanine transglycosylase, an enzymic nucleophile displaces uracil, followed by adenine displacement of the enzymic nucleophile.

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Transglycosylation: a mechanism for RNA modification (and editing?) - PubMed (original) (raw)