Threonine ammonia-lyase

Last updated
L-threonine ammonia-lyase
TD Image 1.png
A 3d cartoon depiction of the threonine deaminase tetramer
EC number
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO

Threonine ammonia-lyase, also commonly referred to as threonine deaminase or threonine dehydratase, is an enzyme responsible for catalyzing the conversion of L-threonine into alpha-ketobutyrate and ammonia. Alpha-ketobutyrate can be converted into L-isoleucine, so threonine ammonia-lyase functions as a key enzyme in BCAA synthesis. [1] It employs a pyridoxal-5'-phosphate cofactor, similar to many enzymes involved in amino acid metabolism. It is found in bacteria, yeast, and plants, though most research to date has focused on forms of the enzyme in bacteria. This enzyme was one of the first in which negative feedback inhibition by the end product of a metabolic pathway was directly observed and studied. [2] The enzyme serves as an excellent example of the regulatory strategies used in amino acid homeostasis.



Threonine ammonia-lyase is a tetramer of identical subunits, and is arranged as a dimer of dimers. Each subunit has two domains: a domain containing the catalytic active site and a domain with allosteric regulatory sites. The two have been shown to be distinct regions, [3] but the regulatory site of one subunit actually interacts with the catalytic site of another subunit. [4] Both domains contain the repeating structural motif of beta sheets surrounded by alpha helices. [5] While the threonine binding site is not perfectly understood, structural studies do reveal how the pyridoxal phosphate cofactor is bound. [4] The PLP cofactor is bonded to a lysine residue by means of a Schiff base, and the phosphate group of PLP is held in place by amine groups derived from a repeating sequence of glycine residues. The aromatic ring is bound to phenylalanine, and the nitrogen on the ring is hydrogen bonded to hydroxyl group-containing residues. [6]

Key residues that interact with PLP within the active site. Generated from 1VE5. TD PLP Site 2.png
Key residues that interact with PLP within the active site. Generated from 1VE5.


The mechanism of threonine ammonia-lyase is analogous to other deaminating PLP enzymes in its use of Schiff base intermediates. [7] Initially, the amine group of threonine attacks the lysine/PLP Schiff base, displacing lysine. After deprotonation of the amino acid alpha carbon and subsequent dehydration (hence the common name threonine dehydratase), a new Schiff base is formed. This Schiff base is replaced by lysine attack, reforming the catalytically active PLP and releasing an initial alkene-containing product. This product tautomerizes, and after hydrolysis of the Schiff base, the final products are generated. [8] [9] After the final alpha-ketobutyrate product is generated, isoleucine is synthesized by progressing through the intermediates alpha-acetohydroxybutyrate to alpha-beta-dihydroxy-beta-methylvalerate, then to alpha-keto-beta-methylvalerate. [10]

The mechanism of threonine ammonia-lyase. PLP and lysine are shown in blue. Mechanism of TD.png
The mechanism of threonine ammonia-lyase. PLP and lysine are shown in blue.


Threonine ammonia-lyase has been shown to not follow Michaelis-Menten kinetics, rather, it is subject to complex allosteric control. [11] The enzyme is inhibited by isoleucine, the product of the pathway it participates in, and is activated by valine, the product of a parallel pathway. [1] Thus, an increase in isoleucine concentration shuts off its production, and an increase in valine concentration diverts starting material (Hydroxyethyl-TPP) away from valine production. The enzyme has two binding sites for isoleucine; one has a high affinity for isoleucine and the other has a low affinity. [12] The binding of isoleucine to the high affinity site increases the binding affinity of the low affinity site, and enzyme deactivation occurs when isoleucine binds to the low affinity site. Valine promotes enzyme activity by competitively binding to the high affinity site, preventing isoleucine from having an inhibitory effect. [12] The combination of these two feedback methods balances the concentration of BCAAs.

A diagram of the feedback regulatory pathways of threonine ammonia-lyase. Regulation of TD.png
A diagram of the feedback regulatory pathways of threonine ammonia-lyase.

Isoforms and other functions

Multiple forms of threonine ammonia-lyase have been observed in a variety of species of organism. In Escherichia coli , a system in which the enzyme has been studied extensively, two different forms of the enzyme are found. One is biosynthetic and resembles the enzyme characteristics presented here, while the other is degradative and functions to generate carbon fragments for energy production. [2] The pair of isoforms has also been observed in other bacteria. In many bacteria, the biodegradative isoform of the enzyme is expressed in anaerobic conditions and is promoted by cAMP and threonine, while the biosynthetic isoform is expressed in aerobic conditions. [13] This allows the bacterium to balance energy stores and inhibit energy-consuming synthetic pathways when energy is not abundant.

In plants, threonine ammonia-lyase is important in defense mechanisms against herbivores and is upregulated in response to abiotic stress. [14] An adapted isoform of the enzyme with unique properties that deter herbivores is expressed in plant leaves. The catalytic domain of this isoform is extremely resistant to proteolysis, while the regulatory domain degrades readily, so upon ingestion by another organism, the threonine deamination capabilities of the enzyme go unchecked. This degrades threonine before the herbivore can absorb it, starving the herbivore of an essential amino acid. [15] Studies of threonine ammonia-lyase in plants have also offered new strategies in the development of GMOs with increased nutritional value by increasing essential amino acid content. [14]

Other more exotic forms of the enzyme have been found that are extremely small in size, but still retain all catalytic and regulatory functions. [4]


There are five major fold types for PLP-dependent enzymes. Threonine ammonia-lyase is a member of the Fold Type II family, also known as the tryptophan synthase family. [7] Though threonine ammonia-lyase does not possess substrate tunneling like tryptophan synthase does, it contains much conserved homology. Threonine ammonia-lyase is most closely related to serine dehydratase, and both possess the same general catalytic mechanism. [9] In fact, threonine ammonia-lyase has been shown to exhibit some specificity towards serine and can convert serine into pyruvate. [2] The regulatory domain of threonine ammonia-lyase is very similar to the regulatory domain of phosphoglycerate dehydrogenase. [4] All of these relationships demonstrate that threonine ammonia-lyase has close evolutionary ties to these enzymes. Due to the degree of conserved structure and sequence in enzymes that recognize amino acids, it is likely that the evolutionary diversity of these enzymes came about by the matching together of individual regulatory and catalytic domains in various ways. [1]

Relevance to humans

Threonine ammonia-lyase is not found in humans. Thus, this is one example of why humans cannot synthesize all 20 proteinogenic amino acids; in this specific case, humans cannot convert threonine into isoleucine and must consume isoleucine in the diet. [1] The enzyme has also been studied in the past as a possible tumor suppressing agent for the previously described reasons, in that it deprives tumor cells of an essential amino acid and kills them, [16] but this treatment has not been utilized.

Related Research Articles

Aspartate carbamoyltransferase Protein family

Aspartate carbamoyltransferase catalyzes the first step in the pyrimidine biosynthetic pathway.

Phosphofructokinase 1 class of enzymes

Phosphofructokinase-1 (PFK-1) is one of the most important regulatory enzymes of glycolysis. It is an allosteric enzyme made of 4 subunits and controlled by many activators and inhibitors. PFK-1 catalyzes the important "committed" step of glycolysis, the conversion of fructose 6-phosphate and ATP to fructose 1,6-bisphosphate and ADP. Glycolysis is the foundation for respiration, both anaerobic and aerobic. Because phosphofructokinase (PFK) catalyzes the ATP-dependent phosphorylation to convert fructose-6-phosphate into fructose 1,6-bisphosphate and ADP, it is one of the key regulatory steps of glycolysis. PFK is able to regulate glycolysis through allosteric inhibition, and in this way, the cell can increase or decrease the rate of glycolysis in response to the cell's energy requirements. For example, a high ratio of ATP to ADP will inhibit PFK and glycolysis. The key difference between the regulation of PFK in eukaryotes and prokaryotes is that in eukaryotes PFK is activated by fructose 2,6-bisphosphate. The purpose of fructose 2,6-bisphosphate is to supersede ATP inhibition, thus allowing eukaryotes to have greater sensitivity to regulation by hormones like glucagon and insulin.


Transamination, a chemical reaction that transfers an amino group to a ketoacid to form new amino acids. This pathway is responsible for the deamination of most amino acids. This is one of the major degradation pathways which convert essential amino acids to non-essential amino acids.

Pyridoxal phosphate Active form of vitamin B6

Pyridoxal phosphate (PLP, pyridoxal 5'-phosphate, P5P), the active form of vitamin B6, is a coenzyme in a variety of enzymatic reactions. The Enzyme commission has catalogued more than 140 PLP-dependent activities, corresponding to ~4% of all classified activities. The versatility of PLP arises from its ability to covalently bind the substrate, and then to act as an electrophilic catalyst, thereby stabilizing different types of carbanionic reaction intermediates.

Glycogen phosphorylase class of enzymes

Glycogen phosphorylase is one of the phosphorylase enzymes. Glycogen phosphorylase catalyzes the rate-limiting step in glycogenolysis in animals by releasing glucose-1-phosphate from the terminal alpha-1,4-glycosidic bond. Glycogen phosphorylase is also studied as a model protein regulated by both reversible phosphorylation and allosteric effects.

Argininosuccinate lyase mammalian protein found in Homo sapiens

ASL is an enzyme that catalyzes the reversible breakdown of argininosuccinate (ASA) producing the amino acid arginine and dicarboxylic acid fumarate. Located in liver cytosol, ASL is the fourth enzyme of the urea cycle and involved in the biosynthesis of arginine in all species and the production of urea in ureotelic species. Mutations in ASL, resulting low activity of the enzyme, increase levels of urea in the body and result in various side effects.

Amino acid synthesis complementary food consist of

Amino acid synthesis is the set of biochemical processes by which the amino acids are produced. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesize all amino acids. For example, humans can only synthesize 11 of the 20 standard amino acids, and in time of accelerated growth, histidine, can be considered an essential amino acid.

Acetolactate synthase class of enzymes

The acetolactate synthase (ALS) enzyme is a protein found in plants and micro-organisms. ALS catalyzes the first step in the synthesis of the branched-chain amino acids.

Cystathionine beta synthase mammalian protein found in Homo sapiens

Cystathionine-β-synthase, also known as CBS, is an enzyme (EC that in humans is encoded by the CBS gene. It catalyzes the first step of the transsulfuration pathway, from homocysteine to cystathionine:

Serine dehydratase

Serine dehydratase or L-serine ammonia lyase (SDH) is in the β-family of pyridoxal phosphate-dependent (PLP) enzymes. SDH is found widely in nature, but its structural and chemical properties vary greatly among species. SDH is found in yeast, bacteria, and the cytoplasm of mammalian hepatocytes. The reaction it catalyzes is the deamination of L-serine to yield pyruvate, with the release of ammonia.

Branched-chain amino acid aminotransferase InterPro Family

Branched-chain amino acid aminotransferase (BCAT), also known as branched-chain amino acid transaminase, is an aminotransferase enzyme (EC which acts upon branched-chain amino acids (BCAAs). It is encoded by the BCAT2 gene in humans. The BCAT enzyme catalyzes the conversion of BCAAs and α-ketoglutarate into branched chain α-keto acids and glutamate.

Ribose-phosphate diphosphokinase class of enzymes

Ribose-phosphate diphosphokinase is an enzyme that converts ribose 5-phosphate into phosphoribosyl pyrophosphate (PRPP). It is classified under EC

Cystathionine gamma-lyase protein-coding gene in the species Homo sapiens

Cystathionine gamma-lyase is an enzyme which breaks down cystathionine into cysteine, α-ketobutyrate, and ammonia. Pyridoxal phosphate is a prosthetic group of this enzyme.

Homoserine dehydrogenase class of enzymes

In enzymology, a homoserine dehydrogenase (EC is an enzyme that catalyzes the chemical reaction

Cystathionine beta-lyase class of enzymes

Cystathionine beta-lyase, also commonly referred to as CBL or β-cystathionase, is an enzyme that primarily catalyzes the following α,β-elimination reaction

Methionine gamma-lyase class of enzymes

Methionine gamma-lyase (MGL) is an enzyme in the γ-family of PLP-dependent enzymes. It degrades sulfur-containing amino acids to α-keto acids, ammonia, and thiols. Because sulfur-containing amino acids play a role in multiple biological processes, the regulation of these amino acids is essential. Additionally, it is crucial to maintain low homocysteine levels for the proper functioning of various pathways and for preventing the toxic effects of the cysteine homologue. Methionine gamma-lyase has been found in several bacteria (Clostridiums porogenes, Pseudomonas ovalis, Pseudomonas putida, Aeromonas sp., Citrobacter intermedius, Brevibacterium linens, Citrobacter freundii, Porphyromonas gingivalis, Treponema denticola), parasitic protozoa (Trichomonas vaginalis, Entamoeba histolytica), and plants (Arabidopsis thaliana).

4-amino-4-deoxychorismate lyase is an enzyme that participates in folate biosynthesis by catalyzing the production of PABA by the following reaction

Arginine decarboxylase class of enzymes

Acid-Induced Arginine Decarboxylase (AdiA), also commonly referred to as arginine decarboxylase, is an enzyme responsible for catalyzing the conversion of L-arginine into agmatine and carbon dioxide. The process consumes a proton in the decarboxylation and employs a pyridoxal-5'-phosphate (PLP) cofactor, similar to other enzymes involved in amino acid metabolism, such as ornithine decarboxylase and glutamine decarboxylase. It is found in bacteria and virus, though most research has so far focused on forms of the enzyme in bacteria. During the AdiA catalyzed decarboxylation of arginine, the necessary proton is consumed from the cell cytoplasm which helps to prevent the over-accumulation of protons inside the cell and serves to increase the intracellular pH. Arginine decarboxylase is part of an enzymatic system in Escherichia coli, Salmonella Typhimurium, and methane-producing bacteria Methanococcus jannaschii that makes these organisms acid resistant and allows them to survive under highly acidic medium.

Diaminopimelate decarboxylase class of enzymes

In enzymology, diaminopimelate decarboxylase, also known as diaminopimelic acid decarboxylase, DAPDC, meso-diaminopimelate decarboxylase, DAP-decarboxylase, and meso-2,6-diaminoheptanedioate carboxy-lyase, is an enzyme that catalyzes the cleavage of carbon-carbon bonds in meso 2,6 diaminoheptanedioate to produce CO2 and L-lysine, the essential amino acid. It employs the cofactor pyridoxal phosphate, also known as PLP, which participates in numerous enzymatic transamination, decarboxylation and deamination reactions.

Cys/Met metabolism PLP-dependent enzyme family

In molecular biology, the Cys/Met metabolism PLP-dependent enzyme family is a family of proteins including enzymes involved in cysteine and methionine metabolism which use PLP (pyridoxal-5'-phosphate) as a cofactor.


  1. 1 2 3 4 5 Berg JM, Tymoczko JL, Stryer L (2012). Biochemistry (7th ed.). New York: W.H. Freeman and Company. ISBN   978-1-4292-7635-1.
  2. 1 2 3 Umbarger HE, Brown B (January 1957). "Threonine deamination in Escherichia coli. II. Evidence for two L-threonine deaminases". Journal of Bacteriology. 73 (1): 105–12. doi:10.1128/jb.73.1.105-112.1957. PMC   289754 . PMID   13405870.
  3. Changeux J (1963). "Allosteric Interactions on Biosynthetic L-threonine Deaminase from E. coli K12". Cold Spring Harbor Symposia on Quantitative Biology. 28: 497–504. doi:10.1101/SQB.1963.028.01.066.
  4. 1 2 3 4 Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E (April 1998). "Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase". Structure. 6 (4): 465–75. doi:10.1016/s0969-2126(98)00048-3. PMID   9562556.
  5. Schneider G, Käck H, Lindqvist Y (January 2000). "The manifold of vitamin B6 dependent enzymes". Structure. 8 (1): R1-6. doi:10.1016/S0969-2126(00)00085-X. PMID   10673430.
  6. 1 2 Goto M (2005). "Crystal Structure of HB8 Threonine deaminase". doi:10.2210/pdb1ve5/pdb.Cite journal requires |journal= (help)
  7. 1 2 Eliot AC, Kirsch JF (2004). "Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations". Annual Review of Biochemistry. 73 (1): 383–415. doi:10.1146/annurev.biochem.73.011303.074021. PMID   15189147.
  8. 1 2 Umbarger HE (2009). "Threonine Deaminases". In Meister A (ed.). Advances in Enzymology and Related Areas of Molecular Biology. Advances in Enzymology - and Related Areas of Molecular Biology. 37. John Wiley & Sons. pp. 349–95. doi:10.1002/9780470122822.ch6. ISBN   978-0-471-59172-6. PMID   4570068.
  9. 1 2 3 Jin J, Hanefeld U (March 2011). "The selective addition of water to C=C bonds; enzymes are the best chemists". Chemical Communications. 47 (9): 2502–10. doi:10.1039/c0cc04153j. PMID   21243161.
  10. Squires CH, Levinthal M, De Felice M (November 1981). "A role for threonine deaminase in the regulation of alpha-acetolactate biosynthesis in Escherichia coli K12". Journal of General Microbiology. 127 (1): 19–25. doi: 10.1099/00221287-127-1-19 . PMID   7040602.
  11. Changeux JP (1961). "The feedback control mechanisms of biosynthetic L-threonine deaminase by L-isoleucine". Cold Spring Harbor Symposia on Quantitative Biology. 26: 313–8. doi:10.1101/SQB.1961.026.01.037. PMID   13878122.
  12. 1 2 Wessel PM, Graciet E, Douce R, Dumas R (December 2000). "Evidence for two distinct effector-binding sites in threonine deaminase by site-directed mutagenesis, kinetic, and binding experiments" (PDF). Biochemistry. 39 (49): 15136–43. doi:10.1021/bi001625c. PMID   11106492.
  13. Luginbuhl GH, Hofler JG, Decedue CJ, Burns RO (October 1974). "Biodegradative L-threonine deaminase of Salmonella typhimurium". Journal of Bacteriology. 120 (1): 559–61. doi:10.1128/jb.120.1.559-561.1974. PMC   245803 . PMID   4370904.
  14. 1 2 Joshi V, Joung JG, Fei Z, Jander G (October 2010). "Interdependence of threonine, methionine and isoleucine metabolism in plants: accumulation and transcriptional regulation under abiotic stress". Amino Acids. 39 (4): 933–47. doi:10.1007/s00726-010-0505-7. PMID   20186554.
  15. Gonzales-Vigil E, Bianchetti CM, Phillips GN, Howe GA (April 2011). "Adaptive evolution of threonine deaminase in plant defense against insect herbivores". Proceedings of the National Academy of Sciences of the United States of America. 108 (14): 5897–902. doi:10.1073/pnas.1016157108. PMC   3078374 . PMID   21436043.
  16. Greenfield RS, Wellner D (August 1977). "Effects of threonine deaminase on growth and viability of mammalian cells in tissue culture and its selective cytotoxicity toward leukemia cells". Cancer Research. 37 (8 Pt 1): 2523–9. PMID   559542.