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MetaCyc Compound: L-pyrrolysine

Synonyms: pyrrolysine, (2S)-2-amino-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]aminohexanoic acid, N6-(4-methyl-1,2-didehydropyrrolidine-5-carboxyl)-L-lysine, N6-((2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl)-L-lysine, N6-(4-methyl-δ-1-pyrroline-5-carboxyl)-L-lysine

Superclasses: an acid all carboxy acids a carboxylate an amino acid an alpha amino acid a non-standard alpha amino acid
an amino acid or its derivative an amino acid an alpha amino acid a non-standard alpha amino acid

Summary:
Pyrrolysine (Pyl or O) is a naturally occurring, genetically coded amino acid. It is used by some methanogenic archaea (and one known bacterium) in several methyltransferases that are involved in methyl transfer from methylated amine compounds to coenzyme M, part of the methanogenesis pathways from these compounds (see methylamine--corrinoid protein Co-methyltransferase, dimethylamine--corrinoid protein Co-methyltransferase and trimethylamine--corrinoid protein Co-methyltransferase). These enzymes catalyze the transfer of the methyl group to dedicated corrinoid proteins. It is believed that the pyrrolysine ring is involved in positioning and displaying the methyl group for attack by the corrinoid cofactor [Hao02].

Pyrrolysine is encoded in mRNA by the UAG codon, which in most organisms is the 'amber' stop codon. Its incorporation into proteins requires two genes - the pylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon, and the pylS gene, which encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with pyrrolysine. Reviewed in [Gaston11].

Chemical Formula: C12H21N3O3

Molecular Weight: 255.32 Daltons

Monoisotopic Molecular Weight: 255.158291556 Daltons

L-pyrrolysine compound structure

SMILES: CC1([CH](C(=O)NCCCCC([N+])C([O-])=O)N=CC1)

InChI: InChI=1S/C12H21N3O3/c1-8-5-7-14-10(8)11(16)15-6-3-2-4-9(13)12(17)18/h7-10H,2-6,13H2,1H3,(H,15,16)(H,17,18)/t8-,9+,10-/m1/s1

InChIKey: InChIKey=ZFOMKMMPBOQKMC-KXUCPTDWSA-N

Unification Links: ChEBI:58499 , KEGG:C16138 , PubChem:23657811

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): 127.54354 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

Not in pathways:
ATP + L-pyrrolysine + a tRNApyl + H+ → AMP + an L-pyrrolysyl-[tRNAPyl] + diphosphate

3-hydroxy-L-homotyrosine biosynthesis :
4-(4-hydroxyphenyl)-2-oxobutanoate + an amino acidL-homotyrosine + a 2-oxo acid

methyl ketone biosynthesis :
a carboxylate + ATP + coenzyme A → an acyl-CoA + AMP + diphosphate

Not in pathways:
an acyl-protein synthetase + a carboxylate + ATP → an acyl-protein thioester + AMP + diphosphate
a carboxylate + GTP + coenzyme A → an acyl-CoA + GDP + phosphate

Reactions known to produce the compound:

L-pyrrolysine biosynthesis :
(2R,3R)-3-methylornithinyl-N6-lysine + NAD+L-pyrrolysine + ammonium + NADH + 2 H+

Not in pathways:
(2R,3R)-3-methylglutamyl-5-semialdehyde-N6-lysine → L-pyrrolysine + H+ + H2O

Not in pathways:
amino acids(n) + H2O → amino acids(n-1) + an α amino acid
an α amino acid ester + H2O → an alcohol + an α amino acid + H+
a protein + H2O → a protein + an α amino acid

3,3'-thiodipropanoate degradation :
3-sulfinopropionate + an acyl-CoA → 3-sulfinopropanoyl-CoA + a carboxylate

dimethylsulfoniopropanoate degradation II (cleavage) :
dimethylsulfoniopropanoate + an acyl-CoA → dimethylsulfoniopropioyl-CoA + a carboxylate

NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) :
an aldehyde + NADP+ + H2O → a carboxylate + NADPH + 2 H+
an aldehyde + NAD+ + H2O → a carboxylate + NADH + 2 H+

phosphatidylcholine resynthesis via glycerophosphocholine :
a phosphatidylcholine + 2 H2O → sn-glycero-3-phosphocholine + 2 a carboxylate + 2 H+

Not in pathways:
a 1-acyl 2-lyso-phosphatidylcholine[periplasmic space] + H2O[periplasmic space]a carboxylate[periplasmic space] + sn-glycero-3-phosphocholine[periplasmic space] + H+[periplasmic space]
an acyl-CoA + H2O → a carboxylate + coenzyme A + H+
an L-1-phosphatidyl-inositol + H2O → a 1-acyl-sn-glycero-3-phospho-D-myo-inositol + a carboxylate + H+
a carboxylic ester + H2O → an alcohol + a carboxylate + H+
an aldehyde + oxygen + H2O → a carboxylate + hydrogen peroxide + H+
an aldehyde + FMNH2 + oxygen → hν + a carboxylate + FMN + H2O + 2 H+
an acylcholine + H2O → choline + a carboxylate + H+
a β-monogalactosyldiacylglycerol + 2 H2O → 2 a carboxylate + 3-β-D-galactosyl-sn-glycerol + 2 H+
an acyl phosphate + H2O → a carboxylate + phosphate + H+
an S-acylglutathione + H2O → a carboxylate + glutathione
an N-acyl-L-aspartate + H2O → L-aspartate + a carboxylate

Reactions known to both consume and produce the compound:

sphingolipid recycling and degradation (yeast) :
a dihydroceramide + H2O ↔ sphinganine + a carboxylate

In Reactions of unknown directionality:

Not in pathways:
a 5-L-glutamyl-[peptide] + an amino acid = a 5-L-glutamyl-amino acid + a peptide

Not in pathways:
eugenol + a carboxylate + NADP+ = a coniferyl ester + NADPH
a 2-acyl 1-lyso-phosphatidylcholine[periplasmic space] + H2O[periplasmic space] = a carboxylate[periplasmic space] + sn-glycero-3-phosphocholine[periplasmic space] + H+[periplasmic space]
an aldehyde + an electron-transfer quinone + H2O = a carboxylate + an electron-transfer quinol + H+
a triacyl-sn-glycerol + H2O = a 1,2-diacyl-sn-glycerol + a carboxylate + H+
a penicillin + H2O = 6-aminopenicillanate + a carboxylate
an aldehyde[periplasmic space] + FAD[periplasmic space] + H2O[periplasmic space] = a carboxylate[periplasmic space] + FADH2[periplasmic space]
a nitrile + 2 H2O = a carboxylate + ammonium
an aliphatic nitrile + 2 H2O = a carboxylate + ammonium
an N-acyl-L-homoserine lactone + H2O = L-homoserine lactone + a carboxylate
an aldehyde + an oxidized unknown electron acceptor + H2O = a carboxylate + an reduced unknown electron acceptor + H+
an N-acylated aromatic-L-amino acid + H2O = a carboxylate + an aromatic L-amino acid
an N-acylated-D-amino acid + H2O = a D-amino acid + a carboxylate
an N-acylated aliphatic-L-amino acid + H2O = a carboxylate + an aliphatic L-amino acid
a D-hexose + an acyl phosphate = a D-hexose-phosphate + a carboxylate
an aldehyde + 2 an oxidized ferredoxin + H2O = a carboxylate + 2 a reduced ferredoxin + 3 H+
an aldehyde + NAD(P)+ + H2O = a carboxylate + NAD(P)H + 2 H+
an N-acyl-D-glutamate + H2O = a carboxylate + D-glutamate
an anilide + H2O = aniline + a carboxylate + H+
a 5'-acylphosphoadenosine + H2O = a carboxylate + AMP + 2 H+
a 3-acylpyruvate + H2O = a carboxylate + pyruvate + H+
an N6acyl-L-lysine + H2O = a carboxylate + L-lysine
an N-acyl-D-aspartate + H2O = a carboxylate + D-aspartate

Credits:
Revised 13-Dec-2011 by Caspi R , SRI International
Revised 13-Feb-2012 by Fulcher CA , SRI International


References

Gaston11: Gaston MA, Jiang R, Krzycki JA (2011). "Functional context, biosynthesis, and genetic encoding of pyrrolysine." Curr Opin Microbiol 14(3);342-9. PMID: 21550296

Hao02: Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK (2002). "A new UAG-encoded residue in the structure of a methanogen methyltransferase." Science 296(5572);1462-6. PMID: 12029132

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Mon Aug 3, 2015, BIOCYC14A.