In enzymology, formate C-acetyltransferase (''pyruvate formate lyase'') () is an

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecule ...

. Pyruvate formate lyase is found in ''

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...

'' and other

organism In biology, an organism () is any life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), taxonomy into groups such as Multicellular o ...

s. It helps regulate

anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: *Adhesive#Anaerobic, Anaerobic ad ...

glucose Glucose is a simple sugar with the molecular formula . Glucose is overall the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, usi ...

metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run c ...

. Using radical non-redox chemistry, it

catalyzes Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycl ...

the reversible conversion of

pyruvate Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic aci ...

and coenzyme-A into

formate Formate ( IUPAC name: methanoate) is the conjugate base of formic acid. Formate is an anion () or its derivatives such as ester of formic acid. The salts and esters are generally colorless.Werner Reutemann and Heinz Kieczka "Formic Acid" in ...

and

acetyl-CoA Acetyl-CoA (acetyl coenzyme A) is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized fo ...

. The reaction occurs as follows: This enzyme belongs to the family of

transferase 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 in hundreds of ...

s, specifically those

acyltransferase Acyltransferase is a type of transferase enzyme that acts upon acyl groups. Examples include: * Glyceronephosphate O-acyltransferase * Lecithin-cholesterol acyltransferase *Long-chain-alcohol O-fatty-acyltransferase In enzymology, a long-chain ...

s transferring groups other than aminoacyl 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 semitrivial ...

of this enzyme class is acetyl-CoA:formate C-acetyltransferase. Other names in common use include pyruvate formate-lyase, pyruvic formate-lyase, and formate acetyltransferase. This enzyme participates in 3

metabolic pathways In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical rea ...

pyruvate metabolism Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic aci ...

propanoate metabolism Propionic acid (, from the Greek words πρῶτος : ''prōtos'', meaning "first", and πίων : ''píōn'', meaning "fat"; also known as propanoic acid) is a naturally occurring carboxylic acid with chemical formula CH3CH2CO2H. It is a liqu ...

, and

butanoate metabolism Butyric acid (; from grc, βούτῡρον, meaning "butter"), also known under the systematic name butanoic acid, is a straight-chain alkyl carboxylic acid with the chemical formula CH3CH2CH2CO2H. It is an oily, colorless liquid with an unple ...

Structural studies

As of late 2007, 8 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , and . Pyruvate formate lyase is a

homodimer In biochemistry, a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. The word ''dimer'' has ...

made of 85 kDa, 759-residue subunits. It has a 10-stranded beta/alpha barrel motif into which is inserted a beta finger that contains major catalytic

residues Residue may refer to: Chemistry and biology * An amino acid, within a peptide chain * Crop residue, materials left after agricultural processes * Pesticide residue, refers to the pesticides that may remain on or in food after they are appli ...

. The active site of the enzyme, elucidated by

x-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angle ...

, holds three essential amino acids that perform catalysis ( Gly734, Cys418, and Cys419), three major residues that hold the substrate pyruvate close by ( Arg435, Arg176, and Ala272), and two flanking hydrophobic residues ( Trp333 and Phe432).Becker A., Fritz-Wolf K., Kabsch W., Knappe J., Schultz S., Volker wagner A.F. Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. 1999 Nat. Struct. Biol. 6: 969–975. Studies have found structural similarities between the active site of pyruvate formate lyase and that of Class I and Class III

ribonucleotide reductase Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase (rNDP), is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of t ...

(RNR) enzymes.

Mechanism

Roles of the three catalytic residues

It has been shown that:Becker, A., Kabsch W. X-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418

thiyl radical In chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a natural science that covers the elements that make up matter to the compounds made of atoms, molecules and ions: their composition, structu ...

for pyruvate cleavage. 2002 J Biol Chem. 277(42): 40036–42.Plaga, W., Wielhaber, G., Wallach, J., Knappe, J. Modification of Cys-418 of pyruvate formate-lyase by methacrylic acid, based on its radical mechanism. 2000 FEBS Lett. 466(1): 45–8. * Gly734 (glycyl radical) – transfers the radical on and off Cys418, via Cys419 * Cys418 (thiyl radical) – does

acylation In chemistry, acylation (or alkanoylation) is the chemical reaction in which an acyl group () is added to a compound. The compound providing the acyl group is called the acylating agent. Because they form a strong electrophile when treated wit ...

chemistry on the carbon atom of the pyruvate

carbonyl In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containin ...

* Cys419 (thiyl radical) – performs

hydrogen-atom A hydrogen atom is an atom of the chemical element hydrogen. The electrically neutral atom contains a single positively charged proton and a single negatively charged electron bound to the nucleus by the Coulomb force. Atomic hydrogen consti ...

transfers

Steps

# The proposed mechanism for pyruvate formate lyase begins with radical transfer from Gly734 to Cys418, via Cys419. # The Cys418 thiyl radical adds covalently to C2 (second carbon atom) of pyruvate, generating an acetyl-enzyme intermediate (which now contains the radical). # The acetyl-enzyme intermediate releases a formyl radical that undergoes hydrogen-atom transfer with Cys419. This generates formate and a Cys419 radical. # coenzyme-A comes in and undergoes hydrogen-atom transfer with the Cys419 radical to generate a coenzyme-A radical. # The coenzyme-A radical then picks up the acetyl group from Cys418 to generate acetyl-CoA, leaving behind a Cys418 radical. # Pyruvate formate lyase can then undergo radical transfer to put the radical back onto Gly734. Note that each step is reversible.

Regulation

Two additional enzymes regulate the “on” and “off” states of pyruvate formate lyase to regulate anaerobic glucose metabolism: pyruvate formate lyase activase (AE) and pyruvate formate lyase deactivase. Activated pyruvate formate lyase allows formation of acetyl-CoA, a small molecule important in the production of energy, when pyruvate is available. Deactivated pyruvate formate lyase, even with substrates present, does not catalyze the reaction. Pyruvate formate lyase activase is part of the radical SAM (

S-adenosylmethionine ''S''-Adenosyl methionine (SAM), also known under the commercial names of SAMe, SAM-e, or AdoMet, is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throu ...

) superfamily. The enzyme turns pyruvate formate lyase “on” by converting Gly734 (G-H) into a Gly734 radical (G^*) via a 5'-

deoxyadenosyl radical A deoxyadenosyl radical is a free radical that is structurally related to adenosine by removal of a 5′-hydroxy group from adenosine. This radical occurs in nature as a reactive intermediate. It is generated by radical SAM enzymes and by some var ...

(via a

radical SAM Radical SAM is a designation for a superfamily of enzymes that use a + cluster">Fe-4Ssup>+ cluster to reductively cleave ''S''-adenosyl-L-methionine (SAM) to generate a radical, usually a 5′- deoxyadenosyl radical (5'-dAdo), as a critical int ...

). For more information about radical SAM activation and

enzymes, see the discussion by Wang et al., 2007. Pyruvate formate lyase deactivase turns pyruvate formate lyase “off” by quenching the Gly734 radical. Furthermore, pyruvate formate lyase is sensitive to molecular

oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as we ...

(O₂), the presence of which shuts the enzyme off.Zhang, W., Wong, KK., Magliozzo, RS., Kozarich, JW. Inactivation of pyruvate formate-lyase by dioxygen: defining the mechanistic interplay of glycine 734 and cysteine 419 by rapid freeze-quench EPR. 2001 Biochemistry 40(13): 4123–30.

References

{{Portal bar, Biology, border=no EC 2.3.1 Enzymes of known structure