Mechanism of ribosome stalling by the AMD1 C-terminal tail arrest peptide

<i>AMD1</i> encodes adenosylmethionine decarboxylase 1 (AMD1), a key enzyme in polyamine biosynthesis. A subset of ribosomes translating the <i>AMD1</i> coding sequence read through the stop codon and pause at a second in-frame stop 384 nucleotides downstream, producing a conserved C-terminal extension (C-tail). Despite growing evidence that such cis-acting elements regulate translation of their genes, the molecular mechanism by which the C-tail mediates ribosome stalling remains unclear. Here, we determined the structure of the ribosome nascent chain complex paused by the AMD1 C-tail which traps eukaryotic release factor 1 (eRF1) with the ATP-binding cassette subfamily E member 1 (ABCE1). The nascent chain forms a molecular clamp that positions an arginine hook in the peptidyl-transferase center, occluding the accommodation of the eRF1 GGQ motif thereby hampering translation termination. Analysis of aggregated ribosome profiling data revealed several genes with a pattern of stop codon readthrough followed by ribosome stalling at a specific location, suggesting that regulatory readthrough-stall mechanisms may not be limited to <i>AMD1</i>.