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Tuesday, August 07, 2012

Monday's Molecule #180

It's Tuesday, so it must be time for Monday's Molecule.... Oops.1

Last week we looked at an important intermediate in the Calvin cycle—the main pathway for fixing carbon dioxide in many species [Monday's Molecule #179]. Today we're going to look at the intermediate in another pathway. Name the molecule, the common name will do.

Discovery of this molecule, and the pathway it's involved in, was an important contribution to understanding basic metabolism in most cells. The enzyme that makes it has been characterized. It's now one of the most widely studied enzymes in biochemistry. The pathway is essential for all species, with a few minor exceptions.

This knowledge has been exploited by technology to an extent never imagined only 50 years ago. Name the technology and how it makes use of what we know about the enzyme and the pathway. For extra bonus points, explain how the molecule got it's root Japanese name.

Post your answers 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. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

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

UPDATE:The molecule is 5-enolpyruvylshikimate 3-phosphate an intermediate in the chorismate pathway and the synthesis of tryptophan, phenylalanine, and tyrosine. The enzyme that produces this product is EPSP synthase and some bacterial versionsof this enzyme are resistant to glyphosate, the active ingredient in the herbicide Roundup®.

The gene for the resistant enzyme can be inserted into crop plants making them resistant to Roundup®.

The winner would have been Ben but I can't identify that person. The winner is Raul A. Félix de Sousa.

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
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa

1. I got confused because yesterday was Simcoe Day.


  1. The molecule is 5-enolpyruvylshikimate-3-phosphate.
    It is an intermediate in the synthesis of chorismate, which is a precursor of aromatic amino acids.

    The enzyme that catalyses the reaction is EPSP synthase.

    A variant of the gene that encodes this enzyme was isolated from an Agrobacterium strain, which is resistant to the herbicide glyphosate. This gene was introduced in soy and other plants resulting in glyphosate-resistant plants.

    According to wikipedia shikimate comes from the Japanese flower shikimi (Illicium anisatum), from which it was first isolated.

  2. Molecule # 180 is 5-enolpyruvylshikimate-3-phosphate (EPSP), a part of the shikimate pathway, which is used by bacteria, fungi and plants to synthesise the aromatic amino acids (among other compounds). The name of this pathway comes from the 'shikimi' (Illicium anisatum), the Japanese flower from which shikimic acid, one of its main constituents was first isolated. Knowledge about the shikimate pathway has found a number of practical technological applications. Metabolic engeneering has allowed the production of shikimic acid, a useful chemical intermediate, by modefied strains of E. coli. Harmless herbicides have been developed, because inhibitors of the enzymes of that pathway have no effect on organisms that lack it.

  3. 5-enolpyruvoylshikimate-3-phosphate (5-Epsp)

    Momsanto's "Roundup" hebicide inhibits 5-Epsp synthetase. Their "Roundup Ready" crops are genetically engineered to contain glyphosate-insensitive form of this enzyme from bacteria.

    "The engineering of transgenic crops resistant to the broad-spectrum herbicide glyphosate has greatly improved agricultural efficiency worldwide. Glyphosate-based herbicides, such as Roundup, target the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the functionality of which is absolutely required for the survival of plants. Roundup Ready plants carry the gene coding for a glyphosate-insensitive form of this enzyme, obtained from Agrobacterium sp. strain CP4. Once incorporated into the plant genome, the gene product, CP4 EPSP synthase, confers crop resistance to glyphosate. Although widely used, the molecular basis for this glyphosate-resistance has remained obscure. We generated a synthetic gene coding for CP4 EPSP synthase and characterized the enzyme using kinetics and crystallography. The CP4 enzyme has unexpected kinetic and structural properties that render it unique among the known EPSP synthases. Glyphosate binds to the CP4 EPSP synthase in a condensed, noninhibitory conformation. Glyphosate sensitivity can be restored through a single-site mutation in the active site (Ala-100-Gly), allowing glyphosate to bind in its extended, inhibitory conformation."

    Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13010-5. Epub 2006 Aug 17.
    Molecular basis for the herbicide resistance of Roundup Ready crops.
    Funke T, Han H, Healy-Fried ML, Fischer M, Schönbrunn E.

    The root name is from shikimic acid which comes from the Japanese flower shikimi (Illicium anisatum), from which it was first isolated.

  4. This is 5-Enolpyruvylshikimate-3-phosphate. Shikimate comes from the Japanese shikimi plant. It is part of the pathway leading to Chorismate synthesis, which is an intermediate in the synthesis of tryptophan, tyrosine and phenylalanine. The popular herbicide Roundup inhibits the synthesis of the molecule, disrupting the production of the aromatic amino acids.

  5. Forgot to add my name:

    Roger Fan