Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme

Abstract

Transfer RNA (tRNA) canonically has the clover-leaf secondary structure with the acceptor, D, anticodon, and T arms, which are folded into the L-shaped tertiary structure. To strengthen the L form, posttranscriptional modifications occur on nucleotides buried within the core, but the modification enzymes are paradoxically inaccessible to them in the L form. In this study, we determined the crystal structure of tRNA bound with archaeosine tRNA-guanine transglycosylase, which modifies G15 of the D arm in the core. The bound tRNA assumes an alternative conformation ("lambda form") drastically different from the L form. All of the D-arm secondary base pairs and the canonical tertiary interactions are disrupted. Furthermore, a helical structure is reorganized, while the rest of the D arm is single stranded and protruded. Consequently, the enzyme precisely locates the exposed G15 in the active site, by counting the nucleotide number from G1 to G15 in the lambda form.

Substrate Specificity for 4-Thiouridine Modification in Escherichia coli

“…For human RNase P, a mini-helix comprising the acceptor and T stems is inactive but becomes an efficient substrate with the insertion of a single nucleotide at position 8 (53). Recently, the crystal structure of the G15 guanine trans- glycosylase from Pyrococcus horikoshii was solved showing that the enzyme binds the novel form of tRNA (55). This intriguing structure involves a rearrangement of the tRNA core to expose nucleotides U8-G22 while preserving the coaxially stacked minihelix comprised of the acceptor and T-stems.…”

“…This intriguing structure involves a rearrangement of the tRNA core to expose nucleotides U8-G22 while preserving the coaxially stacked minihelix comprised of the acceptor and T-stems. It is conceivable as the authors suggest that this alternate form of tRNA is also a preferred substrate for s 4 U modification (55). Binding an alternate tRNA conformation would solve the problem of inaccessibility to U8 in the L-shape tRNA.…”

Crystal Structure of the Apo Forms of ψ 55 tRNA Pseudouridine Synthase from Mycobacterium tuberculosis

“…The C-terminal domain of the MTB-TRUB is a PUA (40) domain, which is commonly found fused to RNA modification enzymes (PUS, RNA methylases, and archaeosine tRNA-guanine transglycosylase (ATG); Ref. 41), but occasionally as a single domain protein. This short domain contains several exposed basic residues.…”

Discovery and Characterization of an Amidinotransferase Involved in the Modification of Archaeal tRNA

“…1) The N-terminal domain in the TgtA2 family is smaller than its counterpart in the arcTGT family by 70 -130 N-terminal residues. 2) Active site and known catalytic residues in the N-terminal domain of arcTGT (12) are not conserved in TgtA2; the general acid/base Asp-95 (P. horikoshii residue numbers) is absent from most TgtA2 sequences, as are the preQ 0 anchoring residues Phe-99, Asp-130, Gln-169, Phe-229, and Met-102, the latter of which stabilizes the cyano group of preQ 0 (12). However, Asp-249, which presumably functions as the catalytic nucleophile in the arcTGT-catalyzed reaction in analogy to the bacTGT, is present in TgtA2. 3) The C1 domain in TgtA2 is much larger than its counterpart in arcTGT (200 residues in TgtA2, but only 40 in arcTGT).…”

“…1C) (11) that is widely conserved in eukaryotic and archaeal RNA modification enzymes. A crystal structure of the Pyrococcus horikoshii arcTGT in complex with tRNA shows that the C-terminal domains interact specifically with the acceptor stem of tRNA (12). In some Archaea, arcTGT is encoded by two open reading frames, with a split occurring between the C1 and C2 domains (13,14).…”