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 shikimi, from which it was first isolated in 1885 by Johan Fredrik Eykman. The elucidation of its structure was made nearly 50 years later.
3-Dehydroquinic acid (DHQ) is the first carbocyclic intermediate of the shikimate pathway. It is created from 3-deoxyarabinoheptulosonate 7-phosphate, a 7-carbon ulonic acid, by the enzyme DHQ synthase. The mechanism of ring closure is complex, but involves an aldol condensation at C-2 and C-7.
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 synthesize 11 of the 20 standard amino acids. These 11 are called the non-essential amino acids).
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.
The enzyme 3-dehydroquinate dehydratase (EC 4.2.1.10) catalyzes the chemical reaction
The enzyme 3-dehydroquinate synthase catalyzes the chemical reaction
Shikimate kinase (EC 2.7.1.71) is an enzyme that catalyzes the ATP-dependent phosphorylation of shikimate to form shikimate 3-phosphate. This reaction is the fifth step of the shikimate pathway, which is used by plants and bacteria to synthesize the common precursor of aromatic amino acids and secondary metabolites. The systematic name of this enzyme class is ATP:shikimate 3-phosphotransferase. Other names in common use include shikimate kinase (phosphorylating), and shikimate kinase II.
The shikimate 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. This pathway is not found in animal cells.
Methanocaldococcus jannaschii is a thermophilic methanogenic archaean in the class Methanococci. It was the first archaeon, and third organism, to have its complete genome sequenced. The sequencing identified many genes unique to the archaea. Many of the synthesis pathways for methanogenic cofactors were worked out biochemically in this organism, as were several other archaeal-specific metabolic pathways.
3-Deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase is the first enzyme in a series of metabolic reactions known as the shikimate pathway, which is responsible for the biosynthesis of the amino acids phenylalanine, tyrosine, and tryptophan. Since it is the first enzyme in the shikimate pathway, it controls the amount of carbon entering the pathway. Enzyme inhibition is the primary method of regulating the amount of carbon entering the pathway. Forms of this enzyme differ between organisms, but can be considered DAHP synthase based upon the reaction that is catalyzed by this enzyme.
2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (EC 1.1.1.302, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase, MjaRED, MJ0671 (gene)) is an enzyme with systematic name 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one:NAD(P)+ oxidoreductase. This enzyme catalyses the following chemical reaction
2-deoxy-scyllo-inosamine dehydrogenase (EC 1.1.1.329, neoA (gene name), kanK (gene name)) is an enzyme with systematic name 2-deoxy-scyllo-inosamine:NAD(P)+ 1-oxidoreductase. This enzyme catalyses the following chemical reaction
UDP-N-acetyl-2-amino-2-deoxyglucuronate dehydrogenase (EC 1.1.1.335, WlbA, WbpB) is an enzyme with systematic name UDP-N-acetyl-2-amino-2-deoxy-alpha-D-glucuronate:NAD+ 3-oxidoreductase. This enzyme catalyses the following chemical reaction:
6-deoxy-5-ketofructose 1-phosphate synthase is an enzyme with systematic name 2-oxopropanal:D-fructose 1,6-bisphosphate glycerone-phosphotransferase. This enzyme catalyses the following chemical reaction
2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase is an enzyme with systematic name L-aspartate 4-semialdehyde:1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate methylglyoxaltransferase. This enzyme catalyses the following chemical reaction
2-deoxy-scyllo-Inosose synthase is an enzyme with systematic name D-glucose-6-phosphate phosphate-lyase (2-deoxy-scyllo-inosose-forming). This enzyme catalyses the following chemical reaction
5'-deoxyadenosine deaminase is an enzyme that catalyzes the conversion of 5′-deoxyadenosine to 5′-deoxyinosine. To a lesser extent, the enzyme also catalyzes the deamination of 5′-methylthioadenosine, S-adenosylhomocysteine, and adenosine. The molecular mass of the DadD enzyme is approximately 230 kDa. DadD maintains 90% of its enzymatic activity after being heated at 60 degrees Celsius for ten minutes. The preferred pH for 5'deoxyadenosine deaminase is 9.0, with the enzyme denaturing at a pH of 11. The DadD enzyme has a preferred substrate of 5'deoxyadenosine, though it will also react with 5′-methylthioadenosine, S-adenosylhomocysteine, and adenosine at lower efficiencies.
