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Pyrrolysine is a naturally occurring genetically coded amino acid. It is coded by the amber stop codon UAG. Structurally it is N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine.
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Pyrrolysine is a lysine derivative encoded by the UAG codon in methylamine methyltransferase genes of Methanosarcina barkeri. Near a methyltransferase gene cluster is the pylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon. The adjacent pylS gene encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with lysine but is not closely related to known lysyl-tRNA synthetases. Homologs of pylS and pylT are found in a Gram-positive bacterium. Charging a tRNA(CUA) with lysine is a likely first step in translating UAG amber codons as pyrrolysine in certain methanogens. Pyrrolysine is the 22nd genetically encoded natural amino acid.
Pyrrolysine is an amino acid used by some bacteria and archaea in enzymes that are part of their methane-producing metabolisms. It is coded for by a UAG codon, which is normally a stop codon named "amber" but whose meaning is modified by the presence of a specific downstream sequence, named PYLIS, which forms a stem-loop in the mRNA, forcing the incorporation of pyrrolysine instead of terminating translation.
See also selenocysteine, an amino acid with a similar mechanism of encoding in other organisms.
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