Ferulic acid decarboxylase

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AnFDC1
AnFDC dimer.png
Dimer of Fdc1 from Aspergillus niger. PDB file : 4ZA4
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EC no. 4.1.1.102
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Ferulic acid decarboxylases (Fdc) are decarboxylase enzymes capable of the reversible decarboxylation of aromatic carboxylic acids such as ferulic acid and cinnamic acid. [1] Fdc's are fungal homologues of the E.coli UbiD enzyme [2] which is involved in ubiquinone biosynthesis. [3] This places Fdc within the wider UbiD enzyme family, representing a distinct clade within the family [2] Presence of fdc1 and the associated pad1 genes (Pad1 homologous to UbiX in E.coli) were shown to be required for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae. [4]

In 2015 the cofactor prFMN was discovered in the active site of Fdc1 from Aspergillus niger (AnFdc) by crystallography, [5] prior to this genetic studies had led to the assumption that both UbiD and UbiX encoded isofunctional decarboxylases. [6] In actuality UbiX/Pad were found to be flavin preyltransferases [7] supplying the prFMN cofactor to UbiD/Fdc [5] where it is utilised for the reversible decarboxylation of alpha-beta unsaturated carboxylic acid substrates. [2] Since the discovery of prFMN AnFDC has become the most well understood representative of the UbiD enzyme family [8]

AnFDC Mechanism

Figure 1. Proposed mechanism for AnFDC. AnFDC Mechanism 2.png
Figure 1. Proposed mechanism for AnFDC.

In the same paper in which the structure of prFMN was deduced in the active site of AnFdc1 there was a proposal for the mechanism by which Fdc1 decarboxylates α,β-unsaturated carboxylic acids. [5] Not all UbiD enzymes decarboxylate acrylic acid substrates and other mechanisms may be at play for alternative substrates. [9] In the case of AnFdc1 it was noted that prFMN displays an azomethine ylide characteristic C4a-N5+=C1’(Figure 1). This is a well-known 1,3-dipole in organic chemistry, positioned in the enzyme active site near to the α,β-unsaturated carboxylic acid substrate which contains a 1,3-dipolarophile. Thus, it was proposed that a 1,3-dipolar cycloaddition mechanism was responsible for the enzymatic decarboxylation. This was confirmed in a later paper. [8]

The mechanism proposed in [5] for 1,3-dipolar cycloaddition by Fdc1 is as follows (intermediates represented in Figure 1):

  1. 1,3-dipolar cycloaddition between prFMNiminium and the α,β-unsaturated substrate leads to a pyrrolidine cycloadduct (Int1)
  2. This pyrrolidine cycloadduct supports simultaneous decarboxylation and ring opening, resulting in the formation of a distinct prFMN-alkene adduct (Int2)
  3. A conserved glutamic acid residue (E282) donates a proton to the alkene moiety, resulting a second pyrrolidine cycloadduct (Int3)
  4. The reaction concludes with cycloelimination of Int3 and the release of the alkene product and CO2

A study went on to present evidence for the 1,3-dipolar cycloaddition, [8] due to suspected turnover of cinnamic acid a crystal structure of AnFdc1 in complex with α-fluorocinnamic acid revealed the substrate Cα and Cβ carbons are located directly above the prFMNiminium C1’ and C4a respectively (shown as Sub in Figure 1 - with cinnamic acid as opposed to α-fluorocinnamic acid). Cinnamic acid was confirmed to bind in a similar manner using inactive AnFdc1 crystals containing FMN. The AnFdc1 E282Q mutant crystallised with cinnamic acid revealed a structure corresponding to the Int2 species, this was taken to mean that progression through the 1,3-dipolarcycloadition cycle was halted as E282 is unable to donate a proton to the alkene moiety.

In order to observe the Int1 and Int3 structures alkyne analogues were used. Like alkenes these compounds can also act as dipolarophiles but cycloaddition would yield a cycloadduct containing a double bond. An inactive AnFdc1 enzyme (with prFMNradical bound) co-crystallised with the phenylpropiolic acid revealed binding in a similar manner to the α-fluorocinnamic acid AnFdc1 and cinnamic acid AnFdc1 with FMN bound (Inhib). An active AnFdc1 enzyme co-crystallised with phenylpropiolic acid revealed clear density for a 3-pyrroline cycloadduct (Int3’) between the alkyne and prFMNiminium. Int3’ represents a structure post decarboxylation, so it was assumed that over the time it took for crystallisation (~24h) the decarboxylation had occurred. Using a rapid soaking procedure, a different cycloadduct was observed that retained the carboxyl moiety (Int1’).

Related Research Articles

<span class="mw-page-title-main">Flavin group</span> Group of chemical compounds

Flavins refers generally to the class of organic compounds containing the tricyclic heterocycle isoalloxazine or its isomer alloxazine, and derivatives thereof. The biochemical source of flavin is the vitamin riboflavin. The flavin moiety is often attached with an adenosine diphosphate to form flavin adenine dinucleotide (FAD), and, in other circumstances, is found as flavin mononucleotide, a phosphorylated form of riboflavin. It is in one or the other of these forms that flavin is present as a prosthetic group in flavoproteins.

Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is the first chemical step in photosynthesis, is called carboxylation, the addition of CO2 to a compound. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).

Aromatic <small>L</small>-amino acid decarboxylase Class of enzymes

Aromatic L-amino acid decarboxylase, also known as DOPA decarboxylase (DDC), tryptophan decarboxylase, and 5-hydroxytryptophan decarboxylase, is a lyase enzyme, located in region 7p12.2-p12.1.

In organic chemistry, a cycloaddition is a chemical reaction in which "two or more unsaturated molecules combine with the formation of a cyclic adduct in which there is a net reduction of the bond multiplicity". The resulting reaction is a cyclization reaction. Many but not all cycloadditions are concerted and thus pericyclic. Nonconcerted cycloadditions are not pericyclic. As a class of addition reaction, cycloadditions permit carbon–carbon bond formation without the use of a nucleophile or electrophile.

The 1,3-dipolar cycloaddition is a chemical reaction between a 1,3-dipole and a dipolarophile to form a five-membered ring. The earliest 1,3-dipolar cycloadditions were described in the late 19th century to the early 20th century, following the discovery of 1,3-dipoles. Mechanistic investigation and synthetic application were established in the 1960s, primarily through the work of Rolf Huisgen. Hence, the reaction is sometimes referred to as the Huisgen cycloaddition. 1,3-dipolar cycloaddition is an important route to the regio- and stereoselective synthesis of five-membered heterocycles and their ring-opened acyclic derivatives. The dipolarophile is typically an alkene or alkyne, but can be other pi systems. When the dipolarophile is an alkyne, aromatic rings are generally produced.

<span class="mw-page-title-main">Flavin adenine dinucleotide</span> Redox-active coenzyme

In biochemistry, flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins, which is involved with several enzymatic reactions in metabolism. A flavoprotein is a protein that contains a flavin group, which may be in the form of FAD or flavin mononucleotide (FMN). Many flavoproteins are known: components of the succinate dehydrogenase complex, α-ketoglutarate dehydrogenase, and a component of the pyruvate dehydrogenase complex.

In organic chemistry, ozonolysis is an organic reaction where the unsaturated bonds are cleaved with ozone. Multiple carbon–carbon bond are replaced by carbonyl groups, such as aldehydes, ketones, and carboxylic acids. The reaction is predominantly applied to alkenes, but alkynes and azo compounds are also susceptible to cleavage. The outcome of the reaction depends on the type of multiple bond being oxidized and the work-up conditions.

<span class="mw-page-title-main">Flavoprotein</span> Protein family

Flavoproteins are proteins that contain a nucleic acid derivative of riboflavin. These proteins are involved in a wide array of biological processes, including removal of radicals contributing to oxidative stress, photosynthesis, and DNA repair. The flavoproteins are some of the most-studied families of enzymes.

<span class="mw-page-title-main">Pyruvate decarboxylase</span> Class of enzymes

Pyruvate decarboxylase is an enzyme that catalyses the decarboxylation of pyruvic acid to acetaldehyde. It is also called 2-oxo-acid carboxylase, alpha-ketoacid carboxylase, and pyruvic decarboxylase. In anaerobic conditions, this enzyme is participates in the fermentation process that occurs in yeast, especially of the genus Saccharomyces, to produce ethanol by fermentation. It is also present in some species of fish where it permits the fish to perform ethanol fermentation when oxygen is scarce. Pyruvate decarboxylase starts this process by converting pyruvate into acetaldehyde and carbon dioxide. Pyruvate decarboxylase depends on cofactors thiamine pyrophosphate (TPP) and magnesium. This enzyme should not be mistaken for the unrelated enzyme pyruvate dehydrogenase, an oxidoreductase, that catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA.

<span class="mw-page-title-main">Azomethine ylide</span>

Azomethine ylides are nitrogen-based 1,3-dipoles, consisting of an iminium ion next to a carbanion. They are used in 1,3-dipolar cycloaddition reactions to form five-membered heterocycles, including pyrrolidines and pyrrolines. These reactions are highly stereo- and regioselective, and have the potential to form four new contiguous stereocenters. Azomethine ylides thus have high utility in total synthesis, and formation of chiral ligands and pharmaceuticals. Azomethine ylides can be generated from many sources, including aziridines, imines, and iminiums. They are often generated in situ, and immediately reacted with dipolarophiles.

Carboxy-lyases, also known as decarboxylases, are carbon–carbon lyases that add or remove a carboxyl group from organic compounds. These enzymes catalyze the decarboxylation of amino acids, beta-keto acids and alpha-keto acids.

Oxidative decarboxylation is a decarboxylation reaction caused by oxidation. Most are accompanied by α- Ketoglutarate α- Decarboxylation caused by dehydrogenation of hydroxyl carboxylic acids such as carbonyl carboxylic acid, malic acid, isocitric acid, etc.

In biochemistry, fatty acid synthesis is the creation of fatty acids from acetyl-CoA and NADPH through the action of enzymes called fatty acid synthases. This process takes place in the cytoplasm of the cell. Most of the acetyl-CoA which is converted into fatty acids is derived from carbohydrates via the glycolytic pathway. The glycolytic pathway also provides the glycerol with which three fatty acids can combine to form triglycerides, the final product of the lipogenic process. When only two fatty acids combine with glycerol and the third alcohol group is phosphorylated with a group such as phosphatidylcholine, a phospholipid is formed. Phospholipids form the bulk of the lipid bilayers that make up cell membranes and surrounds the organelles within the cells.

<span class="mw-page-title-main">Diaminopimelate decarboxylase</span>

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.

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<span class="mw-page-title-main">Umbellic acid</span> Chemical compound

Umbellic acid is a hydroxycinnamic acid. It is an isomer of caffeic acid.

<span class="mw-page-title-main">Flavin prenyltransferase (UbiX)</span>

UbiX is a flavin prenyltransferase, catalysing the addition of dimethylallyl-monophosphate (DMAP) onto the N5 and C6 positions of FMN culminating in the formation of the prenylated FMN (prFMN) cofactor. The enzyme is involved in the ubiquinone biosynthesis pathway in E.coli from where it gets its name UbiX is associated with the UbiD enzymes as prFMN is utilised by UbiD enzymes in their function as reversible decarboxylases. Unusually for a prenyltransferase UbiX is not metal dependent.

Fatty acid photodecarboxylase (FAP) is an enzyme able to decarboxylate saturated and unsaturated free fatty acids into alkane and alkene respectively (carbon dioxide being the co-product). FAP uses continuous blue light to catalyze decarboxylation, making it a photoenzyme (the third well described). The photoenzyme FAP has been initially discovered in the chloroplast membrane of a microalgae called Chlorella variabilis NC64A; The enzyme was also shown to be well conserved in microalgae in general. Others photoenzymes examples include flavin‐dependent DNA‐repair enzyme and protochlorophyllide oxidoreductases.

<span class="mw-page-title-main">Prenylated flavin mononucleotide</span> Chemical compound

Prenylated flavin mononucleotide (prFMN) is a cofactor biosynthesized by the flavin prenyltransferase UbiX and used by UbiD enzymes for reversible decarboxylation reactions. Hence, prFMN is pivotal for catalysis in the ubiquitous microbial UbiD/X system.

In enzymology, a phenacrylate decarboxylase (EC 4.1.1.102) is an enzyme that catalyzes the chemical reaction

References

  1. "FDC1 - Ferulic acid decarboxylase 1 - Aspergillus niger". UniProt.
  2. 1 2 3 Marshall SA, Payne KA, Leys D (October 2017). "The UbiX-UbiD system: The biosynthesis and use of prenylated flavin (prFMN)". Archives of Biochemistry and Biophysics. 632: 209–221. doi:10.1016/j.abb.2017.07.014. PMID   28754323.
  3. Aussel L, Pierrel F, Loiseau L, Lombard M, Fontecave M, Barras F (July 2014). "Biosynthesis and physiology of coenzyme Q in bacteria". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1837 (7): 1004–1011. doi: 10.1016/j.bbabio.2014.01.015 . PMID   24480387.
  4. Mukai N, Masaki K, Fujii T, Kawamukai M, Iefuji H (June 2010). "PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae". Journal of Bioscience and Bioengineering. 109 (6): 564–569. doi:10.1016/j.jbiosc.2009.11.011. PMID   20471595.
  5. 1 2 3 4 Payne KA, White MD, Fisher K, Khara B, Bailey SS, Parker D, et al. (June 2015). "New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition". Nature. 522 (7557): 497–501. Bibcode:2015Natur.522..497P. doi:10.1038/nature14560. PMC   4988494 . PMID   26083754.
  6. Zhang H, Javor GT (June 2003). "Regulation of the isofunctional genes ubiD and ubiX of the ubiquinone biosynthetic pathway of Escherichia coli". FEMS Microbiology Letters. 223 (1): 67–72. doi: 10.1016/S0378-1097(03)00343-4 . PMID   12799002. S2CID   7602116.
  7. White MD, Payne KA, Fisher K, Marshall SA, Parker D, Rattray NJ, et al. (June 2015). "UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis". Nature. 522 (7557): 502–506. Bibcode:2015Natur.522..502W. doi:10.1038/nature14559. PMC   4988493 . PMID   26083743.
  8. 1 2 3 Bailey SS, Payne KA, Saaret A, Marshall SA, Gostimskaya I, Kosov I, et al. (November 2019). "Enzymatic control of cycloadduct conformation ensures reversible 1,3-dipolar cycloaddition in a prFMN-dependent decarboxylase". Nature Chemistry. 11 (11): 1049–1057. Bibcode:2019NatCh..11.1049B. doi:10.1038/s41557-019-0324-8. PMC   6817360 . PMID   31527849.
  9. Leys D (December 2018). "Flavin metamorphosis: cofactor transformation through prenylation". Current Opinion in Chemical Biology. 47: 117–125. doi: 10.1016/j.cbpa.2018.09.024 . PMID   30326424. S2CID   53012607.