Pyridoxal phosphate

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Pyridoxal phosphate
Pyridoxal-phosphate.svg
Idealised skeletal formula
Pyridoxal-phosphate-from-xtal-3D-bs-17.png
Ball-and-stick model based on the crystal structure. [1] [2] Note that the phosphate and pyridine groups have reacted to form a zwitterion and the aldehyde group is hydrated.
Names
Preferred IUPAC name
(4-Formyl-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate
Other names
Pyridoxal 5-phosphate, PAL-P, PLP, Vitamin B6 phosphate
Identifiers
3D model (JSmol)
ChEBI
ChEMBL
ECHA InfoCard 100.000.190 OOjs UI icon edit-ltr-progressive.svg
MeSH Pyridoxal+Phosphate
PubChem CID
UNII
  • O=Cc1c(O)c(C)ncc1COP(O)(O)=O
Properties
C8H10NO6P
Molar mass 247.142 g/mol
Density 1.638±0.06 g/cm3 [3]
Melting point 139 to 142 °C (282 to 288 °F; 412 to 415 K) [4]
Acidity (pKa)1.56 [3]
Pharmacology
A11HA06 ( WHO )
Hazards
Flash point 296.0±32.9 °C [3]
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
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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. [5] 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 reactions, and in certain decarboxylation, deamination, and racemization reactions of amino acids. [6] 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 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. [7] In addition, PLP is used by aminotransferases (or transaminases) that act upon unusual sugars such as perosamine and desosamine. [8] 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). [8]

It is also active in the condensation reaction in heme synthesis.

PLP plays a role in the conversion of levodopa into dopamine, facilitates the conversion of the excitatory neurotransmitter glutamate to the inhibitory neurotransmitter GABA, and allows SAM 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:

Non-classical examples of PLP

PLP is also found on glycogen phosphorylase in the liver, where it is used to break down glycogen 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. [11] 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. [12]

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. [13]

Mechanistic examples: racemization of alanine and elimination of cysteine. PLP mechanism.svg
Mechanistic examples: racemization of alanine and elimination of cysteine.

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). [14] [15] 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 ring nitrogen. [16]

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. [14]

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 for example. PLP is synthesized from pyridoxal by the enzyme pyridoxal kinase, 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. [17]

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 (GAP) and pyruvate. The condensation product of 3-hydroxy-1-aminoacetone phosphate and deoxyxylulose 5-phosphate is pyridoxine 5'-phosphate. The condensation is catalyzed by PNP synthase, encoded by pdxJ, which creates PNP (pyridoxine 5' phosphate). [18] 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. [19] In several species there are two homologues of the E. coliserC gene, generally one in a ser operon (serC), and the other in a pdx operon, in which case it is called pdxF.

Metabolic pathway- pyridoxal 5'-phosphate biosynthesis I v 2.0.svg

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 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 substrate for 4-PHT dehydrogenase (pdxA). [20]

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, this latter molecules is produced by PdxT which catalyzes the production of ammonia from glutamine. PdxS is a (β/α)8 barrel (also known as a TIM-barrel) that forms a dodecamer. [21]

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). [22] In fact, heating NH3 and Glycolaldehyde spontaneously forms a variety of pyridines, including pyridoxal. [22] Under certain conditions, PLP is formed from cyanoacetylene, diacetylene, carbon monoxide, hydrogen, water, and a phosphoric acid. [23]

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, which inhibits a large number of enzymes. [14]

Examples of inhibitors:

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 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. [28]

See also

Related Research Articles

Vitamin B<sub>6</sub> Class of chemically related vitamins

Vitamin B6 is one of the B vitamins, and thus an essential nutrient. The term refers to a group of six chemically similar compounds, i.e., "vitamers", which can be interconverted in biological systems. Its active form, pyridoxal 5′-phosphate, serves as a coenzyme in more than 140 enzyme reactions in amino acid, glucose, and lipid metabolism.

<span class="mw-page-title-main">Transamination</span> Chemical reaction that transfers an amino group to a ketoacid

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 essential amino acids to non-essential amino acids.

<span class="mw-page-title-main">Aminolevulinic acid synthase</span> Class of enzymes

Aminolevulinic acid synthase (ALA synthase, ALAS, or delta-aminolevulinic acid synthase) is an enzyme (EC 2.3.1.37) that catalyzes the synthesis of δ-aminolevulinic acid (ALA) the first common precursor in the biosynthesis of all tetrapyrroles such as hemes, cobalamins and chlorophylls. The reaction is as follows:

<span class="mw-page-title-main">Aspartate transaminase</span> Enzyme involved in amino acid metabolism

Aspartate transaminase (AST) or aspartate aminotransferase, also known as AspAT/ASAT/AAT or (serum) glutamic oxaloacetic transaminase, is a pyridoxal phosphate (PLP)-dependent transaminase enzyme that was first described by Arthur Karmen and colleagues in 1954. AST catalyzes the reversible transfer of an α-amino group between aspartate and glutamate and, as such, is an important enzyme in amino acid metabolism. AST is found in the liver, heart, skeletal muscle, kidneys, brain, red blood cells and gall bladder. Serum AST level, serum ALT level, and their ratio are commonly measured clinically as biomarkers for liver health. The tests are part of blood panels.

<span class="mw-page-title-main">Amino acid synthesis</span> The set of biochemical processes by which amino acids are produced

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.

<span class="mw-page-title-main">Serine hydroxymethyltransferase</span> InterPro Family

Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) (Vitamin B6) dependent enzyme (EC 2.1.2.1) which plays an important role in cellular one-carbon pathways by catalyzing the reversible, simultaneous conversions of L-serine to glycine and tetrahydrofolate (THF) to 5,10-methylenetetrahydrofolate (5,10-CH2-THF). This reaction provides the largest part of the one-carbon units available to the cell.

<span class="mw-page-title-main">Cystathionine beta synthase</span> Mammalian protein found in humans

Cystathionine-β-synthase, also known as CBS, is an enzyme (EC 4.2.1.22) that in humans is encoded by the CBS gene. It catalyzes the first step of the transsulfuration pathway, from homocysteine to cystathionine:

<span class="mw-page-title-main">Pyridoxine 5′-phosphate oxidase</span> Class of enzymes

Pyridoxine 5′-phosphate oxidase is an enzyme, encoded by the PNPO gene, that catalyzes several reactions in the vitamin B6 metabolism pathway. Pyridoxine 5′-phosphate oxidase catalyzes the final, rate-limiting step in vitamin B6 metabolism, the biosynthesis of pyridoxal 5′-phosphate, the biologically active form of vitamin B6 which acts as an essential cofactor. Pyridoxine 5′-phosphate oxidase is a member of the enzyme class oxidases, or more specifically, oxidoreductases. These enzymes catalyze a simultaneous oxidation-reduction reaction. The substrate oxidase enzymes is hydroxylated by one oxygen atom of molecular oxygen. Concurrently, the other oxygen atom is reduced to water. Even though molecular oxygen is the electron acceptor in these enzymes' reactions, they are unique because oxygen does not appear in the oxidized product.

<span class="mw-page-title-main">Serine dehydratase</span>

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 structure and properties vary among species. SDH is found in yeast, bacteria, and the cytoplasm of mammalian hepatocytes. SDH catalyzes the deamination of L-serine to yield pyruvate, with the release of ammonia.

<span class="mw-page-title-main">Transsulfuration pathway</span>

The transsulfuration pathway is a metabolic pathway involving the interconversion of cysteine and homocysteine through the intermediate cystathionine. Two transsulfurylation pathways are known: the forward and the reverse.

In enzymology, a 4-hydroxythreonine-4-phosphate dehydrogenase (EC 1.1.1.262) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Alanine racemase</span>

In enzymology, an alanine racemase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">D-lysine 5,6-aminomutase</span>

In enzymology, D-lysine 5,6-aminomutase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Cystathionine beta-lyase</span> Enzyme

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

<span class="mw-page-title-main">Threonine ammonia-lyase</span>

Threonine ammonia-lyase (EC 4.3.1.19, systematic name L-threonine ammonia-lyase (2-oxobutanoate-forming), also commonly referred to as threonine deaminase or threonine dehydratase, is an enzyme responsible for catalyzing the conversion of L-threonine into α-ketobutyrate and ammonia:

<span class="mw-page-title-main">Diaminopimelate decarboxylase</span> Enzyme decarboxylates diaminopimelate, forming L-lysine

The enzyme diaminopimelate decarboxylase (EC 4.1.1.20) 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.

<span class="mw-page-title-main">Serine C-palmitoyltransferase</span>

In enzymology, a serine C-palmitoyltransferase (EC 2.3.1.50) is an enzyme that catalyzes the chemical reaction:

<span class="mw-page-title-main">Pyridoxine 5'-phosphate synthase</span> Class of enzymes

In enzymology, a pyridoxine 5'-phosphate synthase (EC 2.6.99.2) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Cys/Met metabolism PLP-dependent enzyme family</span>

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.

Glutamate 2,3-aminomutase is an enzyme that belongs to the radical s-adenosyl methionine (SAM) superfamily. Radical SAM enzymes facilitate the reductive cleavage of S-adenosylmethionine (SAM) through the use of radical chemistry and an iron-sulfur cluster. This enzyme family is implicated in the biosynthesis of DNA precursors, vitamin, cofactor, antibiotic and herbicides and in biodegradation pathways. In particular, glutamate 2,3 aminomutase is involved in the conversion of L-alpha-glutamate to L-beta-glutamate in Clostridium difficile. The generalized reaction is shown below:

References

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  2. ↑ Fujiwara T (1973). "The Crystal and Molecular Structure of Vitamin B6 Derivatives. I. Pyridoxal Phosphate Hydrate and Pyridoxal Phosphate Methyl Hemiacetal". Bull. Chem. Soc. Jpn. 46 (3): 863–871. doi: 10.1246/bcsj.46.863 .
  3. 1 2 3 Calculated using Advanced Chemistry Development (ACD/Labs) Software V11.02 (© 1994-2011 ACD/Labs)
  4. ↑ Kozlov ÉI, L'vova MS (1978). "Stability of water-soluble vitamins and coenzymes. Hydrolysis of pyridoxal-5-phosphate in acidic, neutral, and weakly alkaline solutions". Pharmaceutical Chemistry Journal. 11 (11): 1543–9. doi:10.1007/BF00778244. S2CID   1094223.
  5. ↑ Percudani R, Peracchi A (September 2003). "A genomic overview of pyridoxal-phosphate-dependent enzymes". EMBO Reports. 4 (9): 850–4. doi:10.1038/sj.embor.embor914. PMC   1326353 . PMID   12949584.
  6. ↑ Dolphin D, Poulson R, Avramovic O (1986). "Vitamin B6: Pyridoxal Phosphate" (PDF). Coenzymes and Cofactors. Vol. 1, Part B. New York: Wiley Interscience. ISBN   978-0471097853. Archived (PDF) from the original on 2016-03-04. Retrieved 2015-01-04.
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  8. 1 2 Samuel G, Reeves P (November 2003). "Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly". Carbohydrate Research. 338 (23): 2503–19. doi:10.1016/j.carres.2003.07.009. PMID   14670712.
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  14. 1 2 3 Eliot AC, Kirsch JF (2004). "Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations". Annual Review of Biochemistry. 73: 383–415. doi:10.1146/annurev.biochem.73.011303.074021. PMID   15189147. S2CID   36010634.
  15. ↑ Gayathri SC, Manoj N (December 2020). "Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases". Journal of Molecular Biology. 432 (24): 166692. doi:10.1016/j.jmb.2020.10.026. PMID   33122004. S2CID   226205717. Archived from the original on 2022-07-15. Retrieved 2022-10-25.
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  21. ↑ Zhu J, Burgner JW, Harms E, Belitsky BR, Smith JL (July 2005). "A new arrangement of (beta/alpha)8 barrels in the synthase subunit of PLP synthase". The Journal of Biological Chemistry. 280 (30): 27914–23. doi: 10.1074/jbc.M503642200 . PMID   15911615.
  22. 1 2 Austin SM, Waddell TG (May 1999). "Prebiotic synthesis of vitamin B6-type compounds". Origins of Life and Evolution of the Biosphere. 29 (3): 287–96. Bibcode:1999OLEB...29..287A. doi:10.1023/A:1006532518221. PMID   10389266. S2CID   22284565.
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