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Monday, June 18, 2012

Monday's Molecule #174

This is a rather unusual molecule but it's found in many species. You need to identify the molecule AND tell us why it was a significant discovery.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is pyrrolysine, an amino acid found in the proteins of some species of archaebacteria many species of bacteria. Pyrrolysine is made from lysyl-tRNA synthesized in the cytoplasm and attached to a specific pyrrolysyl-tRNA by a specific pyrrolysyl tRNA synthetase. Pyrrolysine is subsequently incorporated into protein during translation. It is inserted at a specific codon (UAG) and counts as the 23 amino acid. The 21st amino acid is N-formylmethionine and the 22nd amino acid is selenocysteine. Today's winner is Raul A. Félix de Sousa who responded before I remembered to turn on comment moderation so I had to delete his response.

Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa


  1. Raul A. Félix de SousaMonday, June 18, 2012 2:31:00 PM

    This comment has been removed by a blog administrator.

  2. This is Pyrrolysine (L in its naturally occurring form)

    Wikipedia defines it:
    "Pyrrolysine (abbreviated as Pyl or O) is a naturally occurring, genetically coded amino acid used by some methanogenic archaea and one known bacterium in enzymes that are part of their methane-producing metabolism. It is similar to lysine, but with an added pyrroline ring linked to the end of the lysine side chain. Produced by a specific tRNA and aminoacyl tRNA synthetase, it forms part of an unusual genetic code in these organisms, and is considered the 22nd proteinogenic amino acid."

    Wow so that is why it was such a significant discovery, a 22nd proteinogenic amino acid, an extra amino acid in the genetic code. Things have certainly changed since I was a biochemistry undergraduate 40 years ago. I keep saying to myself I must learn about the archaeabacteria but I just never get around to it.

  3. This is pyrrolysine, a modified form of lysine found mainly in proteins in methanogenic bacteria.

    It is unusual in that rather than lysine being post-translationally modified is to this molecule, it is incorporated directly into the proteins. Lysine is also present, so there are 21 "natural" amino acids in proteins in these organisms. The genetic code in these organisms is different in this respect.

    Bill Chaney

  4. UPDATE: The molecule is pyrrolysine, an amino acid found in the proteins of some species of archaebacteria. Pyrrolysine is made from lysyl-tRNA that is subsequently incorporated into protein during translation.
    It is also found in eubacteria (Nozawa et al Nature 2009)

    Pyl is synthesized in a tRNA-INdependent manner (Gaston et al Nature 2011; Longstaff et al PNAS 2007)

    The initial paper from Krzycki suggested Lys was aminoacylated to tRNA(Pyl) (Srinivasan et al Science 2002). However work in the Soll lab showed Lys could be attached using a two different LysRS enzymes. (Polycarpo et al Mol Cell 2003).

    Later the Soll lab showed PylRS could directly ligate Pyl to its tRNA (Polycarpo et al PNAS 2004). Very soon after the Krzycki lab showed a similar result (Blight et al Nature 2004). In that Nature paper the contradicting results were only briefly mentioned (blamed on where the His-tag was added, N- vs. C-terminus). I don't think anyone has followed up that hypothesis.

    1. Thank-you for that update. I've read the papers and I'll be adding the biosynthesis of pyrrolysine to the animo acid metabolism chapter in the next edition of my textbook!