RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon

Abstract

Post-transcriptional RNA modifications in the anticodon of transfer RNAs frequently contribute to the high fidelity of protein synthesis. In eubacteria, two genome-encoded transfer RNA (tRNA) species bear the same CAU sequence as the anticodons, which are differentiated by modified cytidines at the wobble positions. The elongator tRNA Met accepts an acetyl moiety at the wobble base to form N 4 -acetylcytidine (ac 4 C): an inherent modification ensures precise decoding of the AUG codon by strengthening CÀG base-pair interaction and concurrently preventing misreading of the near cognate AUA codon. We have determined the crystal structure of tRNA Met cytidine acetyltransferase (TmcA) from Escherichia coli complexed with two natural ligands, acetyl-CoA and ADP, at 2.35 Å resolution. The structure unexpectedly reveals an idiosyncratic RNA helicase module fused with a GCN5-related N-acetyltransferase (GNAT) fold, which intimately crossinteract. Taken together with the biochemical evidence, we further unravelled the function of acetyl-CoA as an enzyme-activating switch, and propose that an RNA helicase motor driven by ATP hydrolysis is used to deliver the wobble base to the active centre of the GNAT domain.

Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation

“…Changing the conserved lysine residue in the Walker A motif (P loop) of the Kre33 helicase domain to an alanine (K289A) (Fig 6B, 6C and 6D) leads to a ~90% reduction in 18S rRNA acetylation (Fig 6D) [16]. Notably, the corresponding lysine residue in the bacterial homolog of Kre33, TmcA (Fig 6C), has been shown to be indispensable for its ATPase-dependent helicase function [29]. How the helicase domain of Kre33 influences the acetylation reaction remains unclear.…”

A Single Acetylation of 18 S rRNA Is Essential for Biogenesis of the Small Ribosomal Subunit in Saccharomyces cerevisiae

“…Recombinant NAT10/hALP (amino acids 164 -834) lacking the N-terminal domains had an ability to acetylate calf thymus histones in vitro in the presence of acetyl-CoA (without ATP), indicating that NAT10/hALP has a histone acetyltransferase activity that might promote hTERT transcription via decondensation of chromatin structure (45). However, based on the crystal structure of TmcA, the N-terminal domain of the recombinant NAT10/hALP that was missing from that construct contains a functionally important region (DUF1726) that constitutes the RNA helicase/ATPase domain required for the tRNA acetyltransferase activity (28,46). Therefore, it remains to be conclusively determined whether full-length NAT10 has an efficient and specific histone acetyltransferase activity.…”

“…Considering that Rra1p has an RNA helicase domain that is essential for ac 4 C1773 formation, Rra1p might unwind the local duplex of helix 45 via its helicase activity to acetylate C1773. A similar mechanism was previously proposed based on a structural study of TmcA, which is responsible for ac 4 C formation in tRNA (46). To investigate the physiological significance of ac 4 C modification in 18 S rRNA, we asked whether rRNA processing might be controlled by cellular energy status.…”

Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible for N4-Acetylcytidine Formation in 18 S Ribosomal RNA (rRNA)

“…According to the crystal structure of E. coli TmcA (16), the RNA helicase domain contains ADP (a hydrolysis product of ATP), whereas the N-acetyltransferase domain interacts with acetyl-CoA. Biochemical and genetic studies of E. coli TmcA revealed that both domains are required for ac 4 C formation in tRNA (15,16). Orthologs of tmcA are widely distributed among archaea and eukaryotes.…”