Pyridoxal phosphate

Source: Wikipedia, the free encyclopedia.
Pyridoxal phosphate
Skeletal formula
Ball-and-stick model
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 Edit this at Wikidata
IUPHAR/BPS
MeSH Pyridoxal+Phosphate
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).
☒N verify (what is checkY☒N ?)

Pyridoxal phosphate (PLP,

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

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

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

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

SAM to be decarboxylated to form propylamine
, which is a precursor to polyamines.

Role in human body

Main article: Vitamin B6

Pyridoxal phosphate has numerous roles in human body. A few examples below:

Non-classical examples of PLP

PLP is also found on

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.

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]

  • 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

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

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. 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 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).[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:

  • 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.[24][25]
  • 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 perhaps might be avoided by supplementing with P5P instead.[26]
  • AlaP (alanine phosphonate) inhibits alanine racemases, but its lack of specificity has prompted further designs of ALR inhibitors.[27]
  • Gabaculine and Vigabatrin inhibit GABA aminotransferase
  • Canaline and 5-fluoromethylornithine inhibit ornithine aminotransferase
  • Amino-oxy SAM inhibits
    ACC synthase

Evolution

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

References

  1. ^ "CSD Entry: PLPHYD10". Cambridge Structural Database: Access Structures. Cambridge Crystallographic Data Centre. 1974. Archived from the original on 2023-11-04. Retrieved 2023-11-04.
  2. doi:10.1246/bcsj.46.863
    .
  3. ^ a b c Calculated using Advanced Chemistry Development (ACD/Labs) Software V11.02 (© 1994-2011 ACD/Labs)
  4. S2CID 1094223
    .
  5. PMID 12949584
    .
  6. ISBN 978-0471097853. Archived
    (PDF) from the original on 2016-03-04. Retrieved 2015-01-04.
  7. PMID 15581583
    .
  8. ^
    PMID 14670712
    .
  9. S2CID 183733461. Archived
    from the original on 2023-11-21. Retrieved 2023-11-21.
  10. ISBN 978-0-8247-0428-5
    .
  11. PMID 16943443
    .
  12. PMID 27835992
    .
  13. PMID 15189147
    .
  14. ^
    S2CID 36010634
    .
  15. S2CID 226205717. Archived
    from the original on 2022-07-15. Retrieved 2022-10-25.
  16. S2CID 10780336
    .
  17. S2CID 28231094
    .
  18. PMID 15242009
    .
  19. PMID 2121717
    .
  20. PMID 21119630
    .
  21. PMID 15911615
    .
  22. ^
    S2CID 22284565
    .
  23. PMID 16730878
    .
  24. S2CID 4262396
    .
  25. PMID 13954890
    .
  26. PMID 28716455
    .
  27. PMID 21637807
    .
  28. PMID 11933250
    .

External links
Retrieved from "https://en.wikipedia.org/w/index.php?title=Pyridoxal_phosphate&oldid=1214622186"