Amino acid synthesis
Amino acid biosynthesis 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 synthesize 11 of the 20 standard amino acids. These 11 are called the non-essential amino acids.
α-Ketoglutarates: glutamate, glutamine, proline, arginine
Most amino acids are synthesized from α-ketoacids, and later transaminated from another amino acid, usually glutamate. The enzyme involved in this reaction is an aminotransferase.Glutamate itself is formed by amination of α-ketoglutarate:
The α-ketoglutarate family of amino acid synthesis begins with α-ketoglutarate, an intermediate in the Citric Acid Cycle. The concentration of α-ketoglutarate is dependent on the activity and metabolism within the cell along with the regulation of enzymatic activity. In E. coli citrate synthase, the enzyme involved in the condensation reaction initiating the Citric Acid Cycle is strongly inhibited by α-ketoglutarate feedback inhibition and can be inhibited by DPNH as well high concentrations of ATP. This is one of the initial regulations of the α-ketoglutarate family of amino acid synthesis.
The regulation of the synthesis of glutamate from α-ketoglutarate is subject to regulatory control of the Citric Acid Cycle as well as mass action dependent on the concentrations of reactants involved due to the reversible nature of the transamination and glutamate dehydrogenase reactions.
The conversion of glutamate to glutamine is regulated by glutamine synthetase and is a key step in nitrogen metabolism. This enzyme is regulated by at least four different mechanisms: 1. Repression and depression due to nitrogen levels; 2. Activation and inactivation due to enzymatic forms ; 3. Cumulative feedback inhibition through end product metabolites; and 4. Alterations of the enzyme due to adenylation and deadenylation. In rich nitrogenous media or growth conditions containing high quantities of ammonia there is a low level of GS, whereas in limiting quantities of ammonia the specific activity of the enzyme is 20-fold higher. The confirmation of the enzyme plays a role in regulation depending on if GS is in the taut or relaxed form. The taut form of GS is fully active but, the removal of manganese converts the enzyme to the relaxed state. The specific conformational state occurs based on the binding of specific divalent cations and is also related to adenylation. The feedback inhibition of GS is due to a cumulative feedback due to several metabolites including L-tryptophan, L-histidine, AMP, CTP, glucosamine-6-phosphate and carbamyl phosphate, alanine, and glycine. An excess of any one product does not individually inhibit the enzyme but a combination or accumulation of all the end products have a strong inhibitory effect on the synthesis of glutamine. Glutamine synthase activity is also inhibited via adenylation. The adenylation activity is catalyzed by the bifunctional adenylyltransferase/adenylyl removal enzyme. Glutamine and a regulatory protein called PII act together to stimulate adenylation.
The regulation of proline biosynthesis can depend on the initial controlling step through negative feedback inhibition. In E. coli, proline allosterically inhibits Glutamate 5-kinase which catalyzes the reaction from L-glutamate to an unstable intermediate L-γ-Glutamyl phosphate.
Arginine synthesis also utilizes negative feedback as well as repression through a repressor encoded by the gene argR. The gene product of argR, ArgR an aporepressor, and arginine as a corepressor affect the operon of arginine biosynthesis. The degree of repression is determined by the concentrations of the repressor protein and corepressor level.
Erythrose 4-phosphate and phosphoenolpyruvate: phenylalanine, tyrosine, and tryptophan
, tyrosine, and tryptophan, the aromatic amino acids, arise from chorismate. The first step, condensation of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate from PEP/E4P, uses three isoenzymes AroF, AroG, and AroH. Each one of these has its synthesis regulated from tyrosine, phenylalanine, and tryptophan, respectively. The rest of the enzymes in the common pathway appear to be synthesized constitutively, except for shikimate kinase, which can be inhibited by shikimate through linear mixed-type inhibition.Tyrosine and phenylalanine are biosynthesized from prephenate, which is converted to an amino acid-specific intermediate. This process is mediated by a phenylalanine or tyrosine specific chorismate mutase-prephenate dehydrogenase. PheA uses a simple dehydrogenase to convert prephenate to phenylpyruvate, while TyrA uses a NAD-dependent dehydrogenase to make 4-hydroxylphenylpyruvate. Both PheA and TyrA are feedback inhibited by their respective amino acids. Tyrosine can also be inhibited at the transcriptional level by the TyrR repressor. TyrR binds to the TyrR boxes on the operon near the promoter of the gene that it wants to repress.
Tryptophan biosynthesis involves conversion of chorismate to anthranilate using anthranilate synthase. This enzyme requires either glutamine as the amino group donor or ammonia itself. Anthranilate synthase is regulated by the gene products of trpE and trpG. trpE encodes the first subunit, which binds to chorismate and moves the amino group from the donor to chorismate. trpG encodes the second subunit, which facilitates the transfer of the amino group from glutamine. Anthranilate synthase is also regulated by feedback inhibition: tryptophan is a co-repressor to the TrpR repressor.
Oxaloacetate/aspartate: lysine, asparagine, methionine, threonine, and isoleucine
The oxaloacetate/aspartate family of amino acids is composed of lysine, asparagine, methionine, threonine, and isoleucine. Aspartate can be converted into lysine, asparagine, methionine and threonine. Threonine also gives rise to isoleucine.The associated enzymes are subject to regulation via feedback inhibition and/or repression at the genetic level. As is typical in highly branched metabolic pathways, additional regulation at each branch point of the pathway. This type of regulatory scheme allows control over the total flux of the aspartate pathway in addition to the total flux of individual amino acids. The aspartate pathway uses L-aspartic acid as the precursor for the biosynthesis of one-fourth of the building block amino acids.
Aspartate
The biosynthesis of aspartate frequently involves the transamination of oxaloacetate.The enzyme aspartokinase, which catalyzes the phosphorylation of aspartate and initiates its conversion into other amino acids, can be broken up into 3 isozymes, AK-I, II and III. AK-I is feed-back inhibited by threonine, while AK-II and III are inhibited by lysine. As a sidenote, AK-III catalyzes the phosphorylation of aspartic acid that is the committed step in this biosynthetic pathway. Aspartate kinase becomes downregulated by the presence of threonine or lysine.
Lysine
is synthesized from aspartate via the diaminopimelate pathway. The initial two stages of the DAP pathway are catalyzed by aspartokinase and aspartate semialdehyde dehydrogenase. These enzymes play a key role in the biosynthesis of lysine, threonine, and methionine. There are two bifunctional aspartokinase/homoserine dehydrogenases, ThrA and MetL, in addition to a monofunctional aspartokinase, LysC. Transcription of aspartokinase genes is regulated by concentrations of the subsequently produced amino acids, lysine, threonine, and methionine. The higher these amino acids concentrations, the less the gene is transcribed. ThrA and LysC are also feed-back inhibited by threonine and lysine. Finally, DAP decarboxylase LysA mediates the last step of the lysine synthesis and is common for all studied bacterial species. The formation of aspartate kinase, which catalyzes the phosphorylation of aspartate and initiates its conversion into other amino acids, is also inhibited by both lysine and threonine, which prevents the formation of the amino acids derived from aspartate. Additionally, high lysine concentrations inhibit the activity of dihydrodipicolinate synthase. So, in addition to inhibiting the first enzyme of the aspartate families biosynthetic pathway, lysine also inhibits the activity of the first enzyme after the branch point, i.e. the enzyme that is specific for lysine's own synthesis.Asparagine
The biosynthesis of asparagine originates with aspartate using a transaminase enzyme. The enzyme asparagine synthetase produces asparagine, AMP, glutamate, and pyrophosphate from aspartate, glutamine, and ATP. In the asparagine synthetase reaction, ATP is used to activate aspartate, forming β-aspartyl-AMP. Glutamine donates an ammonium group, which reacts with β-aspartyl-AMP to form asparagine and free AMP.Image:Asn biosynthesis.svg|frame|center|The biosynthesis of aspartate and asparagine from oxaloacetate.
Two asparagine synthetases are found in bacteria. Both are referred to as the AsnC protein. They are coded for by the genes AsnA and AsnB. AsnC is autogenously regulated, which is where the product of a structural gene regulates the expression of the operon in which the genes reside. The stimulating effect of AsnC on AsnA transcription is downregulated by asparagine. However, the autoregulation of AsnC is not affected by asparagine.
Methionine
Biosynthesis by the transsulfuration pathway starts with aspartic acid. Relevant enzymes include aspartokinase, aspartate-semialdehyde dehydrogenase, homoserine dehydrogenase, homoserine O-transsuccinylase, cystathionine-γ-synthase, Cystathionine-β-lyaseMethionine biosynthesis is subject to tight regulation. The repressor protein MetJ, in cooperation with the corepressor protein S-adenosyl-methionine, mediates the repression of methionine's biosynthesis. The regulator MetR is required for MetE and MetH gene expression and functions as a transactivator of transcription for these genes. MetR transcriptional activity is regulated by homocysteine, which is the metabolic precursor of methionine. It is also known that vitamin B12 can repress MetE gene expression, which is mediated by the MetH holoenzyme.