5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is an

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

produced by plants and

microorganism A microorganism, or microbe, is an organism of microscopic scale, microscopic size, which may exist in its unicellular organism, single-celled form or as a Colony (biology)#Microbial colonies, colony of cells. The possible existence of unseen ...

s. EPSPS

catalyzes Catalysis () is the increase in rate of a chemical reaction due to an added substance known as a catalyst (). Catalysts are not consumed by the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quick ...

the

chemical reaction A chemical reaction is a process that leads to the chemistry, chemical transformation of one set of chemical substances to another. When chemical reactions occur, the atoms are rearranged and the reaction is accompanied by an Gibbs free energy, ...

: : phosphoenolpyruvate (PEP) + 3-phospho

shikimate Shikimic acid, more commonly known as its anionic form shikimate, is a cyclohexene, a cyclitol and a cyclohexanecarboxylic acid. It is an important biochemical metabolite in plants and microorganisms. Its name comes from the Japanese flower ''shik ...

(S3P) phosphate + 5-enolpyruvylshikimate-3-phosphate (EPSP) Thus, the two substrates of this

are phosphoenolpyruvate (PEP) and 3-phosphoshikimate, whereas its two

products Product may refer to: Business * Product (business), an item that can be offered to a market to satisfy the desire or need of a customer. * Product (project management), a deliverable or set of deliverables that contribute to a business solution ...

are

phosphate Phosphates are the naturally occurring form of the element phosphorus. In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthop ...

and 5-enolpyruvylshikimate-3-phosphate. This enzyme is absent from animal genomes, making it an attractive target for

herbicide Herbicides (, ), also commonly known as weed killers, are substances used to control undesired plants, also known as weeds.EPA. February 201Pesticides Industry. Sales and Usage 2006 and 2007: Market Estimates. Summary in press releasMain page f ...

s such as

glyphosate Glyphosate (IUPAC name: ''N''-(phosphonomethyl)glycine) is a broad-spectrum systemic herbicide and crop desiccant. It is an organophosphorus compound, specifically a phosphonate, which acts by EPSP inhibitor, inhibiting the plant enzyme 5-en ...

. A glyphosate-resistant version of the enzyme's gene has been incorporated into

genetically modified crops Genetically modified crops (GM crops) are plants used in agriculture, the DNA of which has been modified using genetic engineering methods. Plant genomes can be engineered by physical methods or by use of '' Agrobacterium'' for the delivery of ...

Nomenclature

The enzyme belongs to the family of

transferase In biochemistry, a transferase is any one of a class of enzymes that catalyse the transfer of specific functional groups (e.g. a methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor). They are involved ...

s, to be specific those transferring

aryl In organic chemistry, an aryl is any functional group or substituent derived from an aromatic ring, usually an aromatic hydrocarbon, such as phenyl and naphthyl. "Aryl" is used for the sake of abbreviation or generalization, and "Ar" is used ...

alkyl In organic chemistry, an alkyl group is an alkane missing one hydrogen. The term ''alkyl'' is intentionally unspecific to include many possible substitutions. An acyclic alkyl has the general formula of . A cycloalkyl group is derived from a cy ...

groups other than

methyl In organic chemistry, a methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms, having chemical formula (whereas normal methane has the formula ). In formulas, the group is often abbreviated as ...

groups. The

systematic name A systematic name is a name given in a systematic way to one unique group, organism, object or chemical substance, out of a specific population or collection. Systematic names are usually part of a nomenclature. A semisystematic name or semitrivi ...

of this enzyme class is phosphoenolpyruvate:3-phosphoshikimate 5-''O''-(1-carboxyvinyl)-transferase. Other names in common use include: * 5-enolpyruvylshikimate-3-phosphate synthase, * 3-enolpyruvylshikimate 5-phosphate synthase, * 3-enolpyruvylshikimic acid-5-phosphate synthetase, * 5′-enolpyruvylshikimate-3-phosphate synthase, * 5-enolpyruvyl-3-phosphoshikimate synthase, * 5-enolpyruvylshikimate-3-phosphate synthetase, * 5-enolpyruvylshikimate-3-phosphoric acid synthase, * enolpyruvylshikimate phosphate synthase, and * 3-phosphoshikimate 1-carboxyvinyl transferase.

Structure

EPSP synthase is a monomeric enzyme with a molecular mass of approximately 46,000. It consists of two domains connected by protein strands that function as a hinge, allowing the two domains to move closer together. When a substrate binds to the enzyme, the conformational change causes the domains to clamp around the substrate at the active site. EPSP synthase is classified into two groups based on sensitivity to glyphosate. Class I enzymes, found in plants and some bacteria, are inhibited by low micromolar concentrations of glyphosate. Class II enzymes, found in other bacteria, are resistant to glyphosate inhibition.

Shikimate pathway

EPSP synthase participates in the biosynthesis of the

aromatic In organic chemistry, aromaticity is a chemical property describing the way in which a conjugated system, conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibits a stabilization stronger than would be expected from conjugati ...

amino acids

phenylalanine Phenylalanine (symbol Phe or F) is an essential α-amino acid with the chemical formula, formula . It can be viewed as a benzyl group substituent, substituted for the methyl group of alanine, or a phenyl group in place of a terminal hydrogen of ...

tyrosine -Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a conditionally essential amino acid with a polar side group. The word "tyrosine" is ...

, and

tryptophan Tryptophan (symbol Trp or W) is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a polar molecule with a non-polar aromat ...

via the

shikimate pathway The shikimate pathway (shikimic acid pathway) is a seven-step metabolic pathway used by bacteria, archaea, fungi, algae, some protozoans, and plants for the biosynthesis of folates and aromatic amino acids (tryptophan, phenylalanine, and tyrosine) ...

in bacteria, fungi, and plants. EPSP synthase is produced only by plants and micro-organisms; the gene coding for it is not in the mammalian

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

Gut flora Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the g ...

of some animals contain EPSPS.

Reaction

EPSP synthase catalyzes the reaction which converts shikimate-3-phosphate plus phosphoenolpyruvate to 5-enolpyruvylshikimate-3-phosphate (EPSP) by way of an

acetal In organic chemistry, an acetal is a functional group with the connectivity . Here, the R groups can be organic fragments (a carbon atom, with arbitrary other atoms attached to that) or hydrogen, while the R' groups must be organic fragments n ...

-like

tetrahedral intermediate A tetrahedral intermediate is a reaction intermediate in which the bond arrangement around an initially double-bonded carbon atom has been transformed from trigonal to tetrahedral. Tetrahedral intermediates result from nucleophilic addition to a c ...

. Basic and acidic

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

s in the

active site In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s ...

are involved in

deprotonation Deprotonation (or dehydronation) is the removal (transfer) of a proton (or hydron, or hydrogen cation), (H+) from a Brønsted–Lowry acid in an acid–base reaction.Henry Jakubowski, Biochemistry Online Chapter 2A3, https://employees.csbsju.ed ...

of the

hydroxyl group In chemistry, a hydroxy or hydroxyl group is a functional group with the chemical formula and composed of one oxygen atom covalently bonded to one hydrogen atom. In organic chemistry, alcohols and carboxylic acids contain one or more hydroxy ...

of PEP and in the proton-exchange steps related to the tetrahedral intermediate itself, respectively. EPSPreactionII

Studies of the

enzyme kinetics Enzyme kinetics is the study of the rates of enzyme catalysis, enzyme-catalysed chemical reactions. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme' ...

for this reaction have determined the specific sequence and energetics of each step of the process. A neutrally charged

lysine Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. Lysine contains an α-amino group (which is in the protonated form when the lysine is dissolved in water at physiological pH), an α-carboxylic acid group ( ...

(lys-22) acts as a general base, deprotonating the

of S3P such that the resulting

oxyanion An oxyanion, or oxoanion, is an ion with the generic formula (where A represents a chemical element and O represents an oxygen atom). Oxyanions are formed by a large majority of the chemical elements. The formulae of simple oxyanions are determine ...

can attack the most

electrophilic In chemistry, an electrophile is a chemical species that forms bonds with nucleophiles by accepting an electron pair. Because electrophiles accept electrons, they are Lewis acids. Most electrophiles are positively charged, have an atom that carr ...

carbon atom of PEP. A

glutamic acid Glutamic acid (symbol Glu or E; known as glutamate in its anionic form) is an α- amino acid that is used by almost all living beings in the biosynthesis of proteins. It is a non-essential nutrient for humans, meaning that the human body can ...

(glu-341) acts as a general acid by donating a

proton A proton is a stable subatomic particle, symbol , Hydron (chemistry), H+, or 1H+ with a positive electric charge of +1 ''e'' (elementary charge). Its mass is slightly less than the mass of a neutron and approximately times the mass of an e ...

. The deprotonated glu-341 then acts as a base, taking back its proton, and the S3P group is kicked off and protonated by the protonated lysine.

Herbicide target

EPSP synthase is the biological target for the herbicide glyphosate. Glyphosate is a

competitive inhibitor Competitive inhibition is interruption of a chemical pathway owing to one chemical substance inhibiting the effect of another by competing with it for binding or bonding. Any metabolic or chemical messenger system can potentially be affected b ...

of EPSP synthase, acting as a

transition state analog Transition state analogs (transition state analogues), are chemical compounds with a chemical structure that resembles the transition state of a substrate molecule in an enzyme-catalyzed chemical reaction. Enzymes interact with a substrate by mea ...

that binds more tightly to the EPSPS-S3P complex than PEP and inhibits the

. This binding leads to inhibition of the enzyme's catalysis and shuts down the pathway. Eventually this results in organism death from lack of aromatic amino acids the organism requires to survive. A version of the enzyme that both was resistant to glyphosate and that was still efficient enough to drive adequate plant growth was identified by

Monsanto The Monsanto Company () was an American agrochemical and agricultural biotechnology corporation founded in 1901 and headquartered in Creve Coeur, Missouri. Monsanto's best-known product is Roundup, a glyphosate-based herbicide, developed ...

scientists after much trial and error in an ''

Agrobacterium ''Agrobacterium'' is a genus of Gram-negative bacteria established by Harold J. Conn, H. J. Conn that uses horizontal gene transfer to cause tumors in plants. ''Agrobacterium tumefaciens'' is the most commonly studied species in this genus. ''Agr ...

'' strain called CP4 (). The strain CP4 was found surviving in a waste-fed column at a glyphosate production facility. The CP4 EPSP synthase enzyme has been engineered into several

Nomenclature

Structure

Shikimate pathway

Reaction

Herbicide target

References

Further reading