Pyridoxal phosphate (PLP,
pyridoxal 5'-
phosphate, P5P), the active form of
vitamin B6, is a
coenzyme in a variety of
enzymatic reactions. The
International Union of Biochemistry and Molecular Biology 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.
Role as a coenzyme
PLP acts as a coenzyme in all
transamination
Transamination is 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 essentia ...
reactions, and in certain
decarboxylation,
deamination
Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases.
In the human body, deamination takes place primarily in the liver, however it can also occur in the kidney. In situations o ...
, and
racemization reactions of
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
s.
The aldehyde group of PLP forms a
Schiff-base linkage (internal
aldimine) with the ε-amino group of a specific lysine group of the
aminotransferase
Transaminases or aminotransferases are enzymes that catalyze a transamination reaction between an amino acid and an α- keto acid. They are important in the synthesis of amino acids, which form proteins.
Function and mechanism
An amino acid ...
enzyme. The α-amino group of the amino acid substrate displaces the ε-amino group of the active-site lysine residue in a process known as transaldimination. The resulting external aldimine can lose a proton, carbon dioxide, or an amino acid sidechain to become a quinonoid intermediate, which in turn can act as a nucleophile in several reaction pathways.
In transamination, after deprotonation the quinonoid intermediate accepts a proton at a different position to become a
ketimine. The resulting ketimine is hydrolysed so that the amino group remains on the complex.
In addition, PLP is used by aminotransferases (or transaminases) that act upon unusual sugars such as
perosamine and
desosamine.
In these reactions, the PLP reacts with
glutamate, which transfers its alpha-amino group to PLP to make pyridoxamine phosphate (PMP). PMP then transfers its nitrogen to the sugar, making an
amino sugar.
PLP is also involved in various beta-elimination reactions such as the reactions carried out by
serine dehydratase and
GDP-4-keto-6-deoxymannose-3-dehydratase (ColD).
It is also active in the condensation reaction in
heme synthesis.
PLP plays a role in the conversion of
levodopa into
dopamine
Dopamine (DA, a contraction of 3,4-dihydroxyphenethylamine) is a neuromodulatory molecule that plays several important roles in cells. It is an organic chemical of the catecholamine and phenethylamine families. Dopamine constitutes about 8 ...
, facilitates the conversion of the excitatory neurotransmitter glutamate to the inhibitory neurotransmitter
GABA, and allows
SAM
Sam, SAM or variants may refer to:
Places
* Sam, Benin
* Sam, Boulkiemdé, Burkina Faso
* Sam, Bourzanga, Burkina Faso
* Sam, Kongoussi, Burkina Faso
* Sam, Iran
* Sam, Teton County, Idaho, United States, a populated place
People and fictional ...
to be decarboxylated to form
propylamine, which is a precursor to polyamines.
Role in human body
Pyridoxal phosphate has numerous roles in human body. A few examples below:
*
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 ...
and
biosynthesis of
serotonin. Pyridoxal phosphate is a
cofactor of
aromatic L-amino acids decarboxylase. This allows for conversion of
5-hydroxytryptophan (5-HTP) into serotonine (5-HT). This reaction takes place in serotonergic neurons.
* Metabolism and biosynthesis of
histamine. Pyridoxal phosphate is a cofactor of
L-histidine decarboxylase
The enzyme histidine decarboxylase (, HDC) is transcribed on chromosome 15, region 21.2, and catalyzes the decarboxylation of histidine to form histamine. In mammals, histamine is an important biogenic amine with regulatory roles in neurotransmiss ...
. This allows for conversion of
histidine
Histidine (symbol His or H) is an essential amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated –NH3+ form under biological conditions), a carboxylic acid group (which is in the ...
into histamine. This reaction takes place in
Golgi apparatus
The Golgi apparatus (), also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles ...
in
mast cells and in
basophils. Next, histamine is stored in granularity in mast cells as a complex with acid residues of
heparin proteoglycan while in basophils as a complex with chondroitine sulfate.
* Metabolism and biosynthesis of
GABA (γ-aminobutyric acid). Pyridoxal phosphate is a cofactor of glutamic acid decarboxylase (GAD). This allows for conversion of glutamate into GABA. Reaction takes place in cytoplasm of termination of GABA-ergic neurons, therefore
vitamin B6 deficiency may cause epileptic
seizures in children. Pyridoxal phosphate also participates in the oxidative
deamination
Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases.
In the human body, deamination takes place primarily in the liver, however it can also occur in the kidney. In situations o ...
of GABA, where it is a cofactor of GABA aminotransferase.
* Metabolism of
ornithine. Pyridoxal phosphate is a cofactor of ornithine carboxylase.
*
Transamination
Transamination is 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 essentia ...
. Pyridoxal phosphate takes part in
decomposition
Decomposition or rot is the process by which dead organic substances are broken down into simpler organic or inorganic matter such as carbon dioxide, water, simple sugars and mineral salts. The process is a part of the nutrient cycle and is ...
and synthesis of
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
s.
Non-classical examples of PLP
PLP is also found on
glycogen phosphorylase in the liver, where it is used to break down
glycogen
Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. The polysaccharide structure represents the main storage form of glucose in the body.
Glycogen functions as one o ...
in
glycogenolysis when
glucagon or
epinephrine signals it to do so. However, this enzyme does not exploit the reactive aldehyde group, but instead utilizes the phosphate group on PLP to perform its reaction.
Although the vast majority of PLP-dependent enzymes form an internal aldimine with PLP via an active site lysine residue, some PLP-dependent enzymes do not have this lysine residue, but instead have a histidine in the active site. In such a case, the histidine cannot form the internal aldimine, and, therefore, the co-factor does not become covalently tethered to the enzyme.
GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) is an example of such an enzyme.
Human
Serine hydroxymethyltransferase 2 regulates one-carbon transfer reactions required for amino acid and nucleotide metabolism, and exists in dimeric and tetrameric forms. The dimeric SHMT2 variant is a potent inhibitor of the BRISC deubiquitylase enzyme complex, which regulates immune-based cell signaling. Recent studies show that SJMT2 tetramerization is induced by PLP. This prevents interaction with the BRISC deubiqutylase complex, potentially linking vitamin B6 levels and metabolism to inflammation.
Catalytic mechanism
The pyridoxal-5′-phosphate-dependent enzymes (PLP enzymes) catalyze myriad reactions. Although the scope of PLP-catalyzed reactions appears to be immense, the unifying principle is the formation of an internal lysine-derived aldimine. Once the amino substrate interacts with the active site, a new Schiff base is generated, commonly referred to as the external aldimine. After this step, the pathway for each PLP-catalyzed reactions diverge.
Specificity
Specificity is conferred by the fact that, of the four bonds of the alpha-carbon of the amino acid aldimine state, the bond perpendicular to the pyridine ring will be broken (
Dunathan Stereoelectronic Hypothesis).
Consequently, specificity is dictated by how the enzymes bind their substrates.
An additional role in specificity is played by the ease of protonation of the
pyridine
Pyridine is a basic (chemistry), basic heterocyclic compound, heterocyclic organic compound with the chemical formula . It is structurally related to benzene, with one methine group replaced by a nitrogen atom. It is a highly flammable, weakl ...
ring nitrogen.
PLP-enzymes
PLP is retained in the active site not only thanks to the lysine, but also thanks to the interaction of the phosphate group and a phosphate binding pocket and to a lesser extent thanks to base stacking of the pyridine ring with an overhanging aromatic residue, generally tyrosine (which may also partake in the acid–base catalysis). Despite the limited requirements for a PLP binding pocket, PLP enzymes belong to only five different families. These families do not correlate well with a particular type of reaction. The five families are classified as fold types followed by a Roman numeral.
[
* Fold Type I — aspartate aminotransferase family
* Fold Type II — tryptophan synthase family
* Fold Type III — alanine racemase family (TIM-barrel)
* Fold Type IV — D-amino acid aminotransferase family
* Fold Type V — glycogen phosphorylase family
]
Biosynthesis
From vitamers
Animals are auxotroph for this enzyme co-factor and require it or an intermediate to be supplemented, hence its classification as a vitamin B6, unlike MoCo or CoQ10
Coenzyme Q, also known as ubiquinone and marketed as CoQ10, is a coenzyme family that is ubiquitous in animals and most bacteria (hence the name ubiquinone). In humans, the most common form is coenzyme Q10 or ubiquinone-10.
It is a 1,4-benzoq ...
for example. PLP is synthesized from pyridoxal by the enzyme pyridoxal kinase
In enzymology, a pyridoxal kinase () is an enzyme that catalysis, catalyzes the chemical reaction
:ATP + pyridoxal \rightleftharpoons ADP + pyridoxal 5'-phosphate
Thus, the two substrate (biochemistry), substrates of this enzyme are adenosine tri ...
, requiring one ATP molecule. PLP is metabolized in the liver.
Prototrophy
Two natural pathways for PLP are currently known: one requires deoxyxylulose 5-phosphate (DXP), while the other does not, hence they are known as DXP-dependent and DXP-independent. These pathways have been studied extensively in ''Escherichia coli'' and ''Bacillus subtilis'', respectively. Despite the disparity in the starting compounds and the different number of steps required, the two pathways possess many commonalities.
DXP-dependent biosynthesis
The DXP-dependent biosynthetic route requires several steps and a convergence of two branches, one producing 3-hydroxy-1-aminoacetone phosphate from erythrose 4-phosphate, while the other (single enzyme) producing deoxyxylulose 5-phosphate (DXP) from glyceraldehyde 3-phosphate
Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, is a metabolite that occurs as an intermediate in several central pathways of all organisms.Nelson, D ...
(GAP) and pyruvate. The condensation product of 3-hydroxy-1-aminoacetone phosphate and deoxyxylulose 5-phosphate is pyridoxine 5'-phosphate
Pyridoxine, is a form of vitamin B6 found commonly in food and used as a dietary supplement. As a supplement it is used to treat and prevent pyridoxine deficiency, sideroblastic anaemia, pyridoxine-dependent epilepsy, certain metabolic disorder ...
. The condensation is catalyzed by PNP synthase, encoded by ''pdxJ'', which creates PNP (pyridoxine 5' phosphate). The final enzyme is PNP oxidase (''pdxH''), which catalyzes the oxidation of the 4' hydroxyl group to an aldehyde using dioxigen, resulting in hydrogen peroxide.
The first branch is catalyzed in ''E. coli'' by enzymes encoded by ''epd'', ''pdxB'', ''serC'' and ''pdxA''. These share mechanistical similarities and homology with the three enzymes in serine biosynthesis (''serA'' (homologue of ''pdxB''), ''serC'', ''serB'' — however, ''epd'' is a homologue of ''gap''), which points towards a shared evolutionary origin of the two pathways. In several species there are two homologues of the ''E. coli'' ''serC'' gene, generally one in a ser operon (''serC''), and the other in a pdx operon, in which case it is called ''pdxF''.
A "serendipitous pathway" was found in an overexpression library that could suppress the auxotrophy caused by the deletion of pdxB (encoding erythronate 4 phosphate dehydrogenase) in ''E. coli''. The serendipitous pathway was very inefficient, but was possible due to the promiscuous activity
Enzyme promiscuity is the ability of an enzyme to catalyse a fortuitous side reaction in addition to its main reaction. Although enzymes are remarkably specific catalysts, they can often perform side reactions in addition to their main, native cata ...
of various enzymes. It started with 3-phosphohydroxypyruvate (the product of the ''serA''-encoded enzyme in serine biosynthesis) and did not require erythronate-4-phosphate. 3PHP was dephosphorylated, resulting in an unstable intermediate that decarboxylates spontaneously (hence the presence of the phosphate in the serine biosynthetic pathway) to glycaldehyde. Glycaldehyde was condensed with glycine and the phosphorylated product was 4-phosphohydroxythreonine (4PHT), the canonical substate for 4-PHT dehydrogenase (''pdxA'').
DXP-independent biosynthesis
The DXP-independent PLP-biosynthetic route consists of a step catalyzed by PLP-synthase, an enzyme composed of two subunits. PdxS catalyzes the condensation of ribulose 5-phosphate, glyceraldehyde-3-phosphate, and ammonia
Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogeno ...
, this latter molecules is produced by PdxT which catalyzes the production of ammonia from glutamine
Glutamine (symbol Gln or Q) is an α-amino acid that is used in the biosynthesis of proteins. Its side chain is similar to that of glutamic acid, except the carboxylic acid group is replaced by an amide. It is classified as a charge-neutral ...
. PdxS is a (β/α)8 barrel (also known as a TIM-barrel) that forms a dodecamer.
Abiotic synthesis
The widespread utilization of PLP in central metabolism, especially in amino acid biosynthesis, and its activity in the absence of enzymes, suggests PLP may be a "prebiotic" compound—that is, one that predates the origin of organic life (not to be confused with prebiotic compounds, substances which serve as a food source for beneficial bacteria).
In fact, heating NH3 and Glycolaldehyde spontaneously forms a variety of pyridines, including pyridoxal.[ Under certain conditions, PLP is formed from cyanoacetylene, diacetylene, carbon monoxide, hydrogen, water, and a phosphoric acid.
]
Inhibitors
Several inhibitors of PLP enzymes are known.
One type of inhibitor forms an electrophile with PLP, causing it to irreversibly react with the active site lysine. Acetylenic compounds (e.g. propargylglycine) and vinylic compounds (e.g. vinylglycine) are such inhibitors.
A different type of inhibitor inactivates PLP, and such are α-methyl and amino-oxy substrate analogs (e.g. α-methylglutamate). Still other inhibitors have good leaving groups that nucleophilically attack the PLP. Such is chloroalanine
Chloroalanine (3-chloroalanine) is an unnatural amino acid with the formula ClCH2CH(NH2)CO2H. It is a white, water-soluble solid. The compound is usually derived from chlorination of serine. The compound is used in the synthesis of other amino ac ...
, which inhibits a large number of enzymes.[
Examples of inhibitors:
* Levothyroxine In rats given only 10 µg of D , L-thyroxine daily for 15 days, liver cysteine desulfhydrase activity disappears and serine and threonine dehydrase and alanine glutamate transaminase activities decrease about 40%. Either in vivo feeding of pyridoxal-5-phosphate or in vitro addition of the coenzyme to the liver preparations restores full activity to all these enzymes, and the slight in vitro inhibition in the presence of 10−5 M thyroxine is also reversed by pyridoxal-5-phosphate.
* The inactive form pyridoxine competitively inhibits the active pyridoxal-5'-phosphate. Consequently, symptoms of vitamin B6 supplementation in the pyridoxine form can mimic those of vitamin B6 deficiency; an effect which can be avoided by supplementing with P5P instead.
* AlaP (alanine phosphonate) inhibits alanine racemases, but its lack of specificity has prompted further designs of ALR inhibitors.
* ]Gabaculine
Gabaculine is a naturally occurring neurotoxin first isolated from the bacteria ''Streptomyces toyacaensis'', which acts as a potent and irreversible GABA transaminase inhibitor, and also a GABA reuptake inhibitor. Gabaculine is also known as 3-am ...
and Vigabatrin inhibit GABA aminotransferase
* Canaline and 5-fluoromethylornithine inhibit ornithine aminotransferase
* Amino-oxy SAM inhibits ACC synthase
Evolution
Pyridoxal-5-phosphate (vitamin B6)-dependent enzymes have multiple evolutionary origins. The overall B6 enzymes diverged into four independent evolutionary lines: α family (i.e. aspartate aminotransferase), β family ( serine dehydratase),D- alanine aminotransferase family and the alanine racemase family. An example of the evolutionary similarity in the Beta family is seen in the mechanism. The β enzymes are all lyases
In biochemistry, a lyase is an enzyme that catalyzes the breaking (an elimination reaction) of various chemical bonds by means other than hydrolysis (a substitution reaction) and oxidation, often forming a new double bond or a new ring structure. ...
and catalyze reactions where Cα and Cβ participate. Overall, in the PLP-dependent enzymes, the PLP in every case is covalently attached via an imine bond to the amino group in the active site.
See also
* Aromatic-L-amino-acid decarboxylase
* Ornithine decarboxylase
References
External links
*
{{DEFAULTSORT:Pyridoxal Phosphate
B vitamins
Organophosphates
3-Hydroxypropenals
Aromatic ketones