Lipoyl synthase

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Lipoyl synthase
Identifiers
EC no. 2.8.1.8
CAS no. 189398-80-9
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This image displays the crystal structure of M. tuberculosis lipoyl synthase. The 11 a-helices are displayed in red and the 7 b sheets are displayed in blue. The DTV cofactor is displayed in yellow. The two [4Fe-4S] clusters are displayed as cubic structures within the enzyme. PBD Code: 5EXI Lipoyl Synthase.png
This image displays the crystal structure of M. tuberculosis lipoyl synthase. The 11 α-helices are displayed in red and the 7 β sheets are displayed in blue. The DTV cofactor is displayed in yellow. The two [4Fe-4S] clusters are displayed as cubic structures within the enzyme. PBD Code: 5EXI

Lipoyl synthase is an enzyme that belongs to the radical SAM (S-adenosyl methionine) family. Within the radical SAM superfamily, lipoyl synthase is in a sub-family of enzymes that catalyze sulfur insertion reactions. The enzymes in this subfamily differ from general radical SAM enzymes, as they contain two 4Fe-4S clusters. From these clusters, the enzymes obtain the sulfur groups that will be transferred onto the corresponding substrates. [1] This particular enzyme participates in the final step of lipoic acid metabolism, transferring two sulfur atoms from its 4Fe-4S cluster onto the protein N6-(octanoyl)lysine through radical generation. This enzyme is usually localized to the mitochondria. Two organisms that have been extensively studied with regards to this enzyme are Escherichia coli and Mycobacterium tuberculosis. It is currently being studied in other organisms including yeast, plants, and humans.

Contents

Nomenclature

The systematic name of this enzyme class is protein N6-(octanoyl)lysine:sulfur sulfurtransferase. Other names in common use include:

Structure

The sequence length of M. tuberculosis lipoyl synthase is approximately 331 amino acids. The structure is composed of 11 α-helices and 7 β sheets, with multiple loop structures connecting the other components. The two [4Fe-4S] clusters are located within the structure, appearing in three-dimensional cubic shape. A molecule of DTV ((2S,3S)-1,4-Dimercaptobutane-2,3-diol), more commonly known as DTT (dithiothreitol), is also present within the structure. This molecule is responsible for protecting thiol groups from oxidation. The molecule is surrounded by water molecules as well, which form hydrogen bonds with side residues to stabilize the structure. The enzyme's structure is shown.

Mechanism of lipoyl synthase

This image displays the auxillery [4Fe-4S] cluster adding a sulfur onto a lysine residue that is part of the protein. This causes the cluster to become [4Fe-3S] and the modified lysine is formed (labeled XOK). The 5'-deoxyadenosine is also pictured, along with the coordinate cysteine residues . PBD Code: 5EXK Modification of lysine by cluster.png
This image displays the auxillery [4Fe-4S] cluster adding a sulfur onto a lysine residue that is part of the protein. This causes the cluster to become [4Fe-3S] and the modified lysine is formed (labeled XOK). The 5'-deoxyadenosine is also pictured, along with the coordinate cysteine residues . PBD Code: 5EXK

As previously mentioned, lipoyl synthase is a member of a subfamily of the radical SAM(S-adenosyl methionine) enzyme family, which use a [4Fe-4S] cluster cofactor. This cofactor is used by this enzyme to produce 5'-deoxyadenosyl 5'-radical (5'-dA). [2] Lipoyl synthase itself uses this radical to abstract hydrogens from the 6th and 8th carbons of the protein N6(octanoyl)lysine substrate. Two sulfurs from one of lipoyl synthase's two [4Fe-4S] clusters, known as the auxiliary cluster, are then attached to the 6th and 8th carbons in place of the abstracted hydrogens.The protein N6-(octanoyl)lysine substrate is then converted into the protein N6-(lipoyl)lysine. The figure on the right depicts the lysine interacting with the auxiliary cluster to add one sulfur, which then becomes an [4Fe-3S] cluster. The other [4Fe-4S] cluster is coordinated by the radical SAM motif of the enzyme (CxxxCxxC) and participates in radical SAM characteristic chemistry to activate the substrate for subsequent sulfur insertion. [3] The three substrates of this enzyme are N6-(octanoyl)lysine, sulfur, and S-adenosyl-L-methionine. The three products are N6-(lipoyl)lysine, L-methionine, and 5'-deoxyadenosine. Below displays the overall reaction catalyzed by lipoyl synthase, with the structures of each substrate and product.

This image depicts the enzyme catalyzed reaction involving lipoyl synthase. The lysine is a residue a part of the polypeptide backbone of the protein. The sulfur molecules comes from the [4Fe-4S] auxiliary cluster. Lipoyl Synthase mechanism.png
This image depicts the enzyme catalyzed reaction involving lipoyl synthase. The lysine is a residue a part of the polypeptide backbone of the protein. The sulfur molecules comes from the [4Fe-4S] auxiliary cluster.

Importance of lipoyl synthase

This enzyme participates in lipoic acid metabolism, where it performs the final step in lipoic acid biosynthesis. Lipoic acid is a cofactor that has different functions within different organisms. [4] The lipoic acid generation in yeast cells increases the number of divisions in the cells as well as protects yeast cells from hydrogen peroxide. [5] Lipoic acid is an important co-factor in many enzyme systems, and one of them is the pyruvate dehydrogenase complex. [6] Studies that repressed the function of lipoyl synthase in Arabidopsis thaliana seeds showed that this did not have adverse effects on seed growth and weight, but shortened the generation time as well as the flowering time of the plants. Repression resulted in earlier flowering times and decreased the generation times between seeds by almost 10%. [7]

Possible side effects of lipoyl synthase in plants

Overexpression of this enzyme in sunflower plants has been found to eventually sequester the amount of SAM present in transgenic Arabidopsis plants. SAM is a molecule that is required in other enzymatic complexes found in this plant as well, as well as the overall structure of the plant, so this sequestration may cause a reduction in the fatty acid biosynthesis in the Arabidopsis seeds. [8]

Related Research Articles

<span class="mw-page-title-main">Methionine</span> Sulfur-containing amino acid

Methionine is an essential amino acid in humans. As the precursor of other amino acids such as cysteine and taurine, versatile compounds such as SAM-e, and the important antioxidant glutathione, methionine plays a critical role in the metabolism and health of many species, including humans. It is encoded by the codon AUG.

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

Lipoic acid (LA), also known as α-lipoic acid, alpha-lipoic acid (ALA) and thioctic acid, is an organosulfur compound derived from caprylic acid (octanoic acid). ALA is made in animals normally, and is essential for aerobic metabolism. It is also manufactured and is available as a dietary supplement in some countries where it is marketed as an antioxidant, and is available as a pharmaceutical drug in other countries. Lipoate is the conjugate base of lipoic acid, and the most prevalent form of LA under physiological conditions. Only the (R)-(+)-enantiomer (RLA) exists in nature and is essential for aerobic metabolism because RLA is an essential cofactor of many enzyme complexes.

Iron–sulfur proteins are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur clusters are found in a variety of metalloproteins, such as the ferredoxins, as well as NADH dehydrogenase, hydrogenases, coenzyme Q – cytochrome c reductase, succinate – coenzyme Q reductase and nitrogenase. Iron–sulfur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe–S clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally, some Fe–S proteins regulate gene expression. Fe–S proteins are vulnerable to attack by biogenic nitric oxide, forming dinitrosyl iron complexes. In most Fe–S proteins, the terminal ligands on Fe are thiolate, but exceptions exist.

<span class="mw-page-title-main">Methyltransferase</span> Group of methylating enzymes

Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Rossmann fold for binding S-Adenosyl methionine (SAM). Class II methyltransferases contain a SET domain, which are exemplified by SET domain histone methyltransferases, and class III methyltransferases, which are membrane associated. Methyltransferases can also be grouped as different types utilizing different substrates in methyl transfer reactions. These types include protein methyltransferases, DNA/RNA methyltransferases, natural product methyltransferases, and non-SAM dependent methyltransferases. SAM is the classical methyl donor for methyltransferases, however, examples of other methyl donors are seen in nature. The general mechanism for methyl transfer is a SN2-like nucleophilic attack where the methionine sulfur serves as the leaving group and the methyl group attached to it acts as the electrophile that transfers the methyl group to the enzyme substrate. SAM is converted to S-Adenosyl homocysteine (SAH) during this process. The breaking of the SAM-methyl bond and the formation of the substrate-methyl bond happen nearly simultaneously. These enzymatic reactions are found in many pathways and are implicated in genetic diseases, cancer, and metabolic diseases. Another type of methyl transfer is the radical S-Adenosyl methionine (SAM) which is the methylation of unactivated carbon atoms in primary metabolites, proteins, lipids, and RNA.

Lysine 2,3-aminomutase is a radical SAM enzyme that facilitates the conversion of the amino acid lysine to beta-lysine. It accomplishes this interconversion using three cofactors and a 5'-deoxyadenosyl radical formed in a S-Adenosyl methionine (SAM) activated radical reaction pathway.[1] The generalized reaction is shown below:

<span class="mw-page-title-main">Adenylyl-sulfate reductase</span> Class of enzymes

Adenylyl-sulfate reductase is an enzyme that catalyzes the chemical reaction of the reduction of adenylyl-sulfate/adenosine-5'-phosphosulfate (APS) to sulfite through the use of an electron donor cofactor. The products of the reaction are AMP and sulfite, as well as an oxidized electron donor cofactor.

<span class="mw-page-title-main">1-Aminocyclopropane-1-carboxylate synthase</span> Class of enzymes

The enzyme aminocyclopropane-1-carboxylic acid synthase catalyzes the synthesis of 1-Aminocyclopropane-1-carboxylic acid (ACC), a precursor for ethylene, from S-Adenosyl methionine, an intermediate in the Yang cycle and activated methyl cycle and a useful molecule for methyl transfer:

<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">Biotin synthase</span> Enzyme

Biotin synthase (BioB) is an enzyme that catalyzes the conversion of dethiobiotin (DTB) to biotin; this is the final step in the biotin biosynthetic pathway. Biotin, also known as vitamin B7, is a cofactor used in carboxylation, decarboxylation, and transcarboxylation reactions in many organisms including humans. Biotin synthase is an S-Adenosylmethionine (SAM) dependent enzyme that employs a radical mechanism to thiolate dethiobiotin, thus converting it to biotin.

In enzymology, a lipoyl(octanoyl) transferase (EC 2.3.1.181) is an enzyme that catalyzes the chemical reaction

Spore photoproduct lyase is a radical SAM enzyme that repairs DNA cross linking of thymine bases caused by UV-radiation. There are several types of thymine cross linking, but SPL specifically targets 5-thyminyl-5,6-dihydrothymine, which is also called spore photoproduct (SP). Spore photoproduct is the predominant type of thymine crosslinking in germinating endospores, which is why SPL is unique to organisms that produce endospores, such as Bacillus subtilis. Other types of thymine crosslinking, such as cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), are less commonly formed in endospores. These differences in DNA crosslinking are a function of differing DNA structure. Spore genomic DNA features many DNA binding proteins called small acid soluble proteins, which changes the DNA from the traditional B-form conformation to an A-form conformation. This difference in conformation is believed to be the reason why dormant spores predominantly accumulate SP in response to UV-radiation, rather than other forms of cross linking. Spores cannot repair cross-linking while dormant, instead the SPs are repaired during germination to allow the vegetative cell to function normally. When not repaired, spore photoproduct and other types of crosslinking can cause mutations by blocking transcription and replication past the point of the crosslinking. The repair mechanism utilizing spore photoproduct lyase is one of the reasons for the resilience of certain bacterial spores.

Radical SAM is a designation for a superfamily of enzymes that use a [4Fe-4S]+ cluster to reductively cleave S-adenosyl-L-methionine (SAM) to generate a radical, usually a 5′-deoxyadenosyl radical (5'-dAdo), as a critical intermediate. These enzymes utilize this radical intermediate to perform diverse transformations, often to functionalize unactivated C-H bonds. Radical SAM enzymes are involved in cofactor biosynthesis, enzyme activation, peptide modification, post-transcriptional and post-translational modifications, metalloprotein cluster formation, tRNA modification, lipid metabolism, biosynthesis of antibiotics and natural products etc. The vast majority of known radical SAM enzymes belong to the radical SAM superfamily, and have a cysteine-rich motif that matches or resembles CxxxCxxC. rSAMs comprise the largest superfamily of metal-containing enzymes.

Octanoyl-(GcvH):protein N-octanoyltransferase (EC 2.3.1.204, LIPL, octanoyl-[GcvH]:E2 amidotransferase, YWFL (gene)) is an enzyme with systematic name (glycine cleavage system H)-N6-octanoyl-L-lysine:(lipoyl-carrier protein)-N6-L-lysine octanoyltransferase. This enzyme catalyses the following chemical reaction

<span class="mw-page-title-main">Phosphomethylpyrimidine synthase</span>

Phosphomethylpyrimidine synthase is an enzyme with systematic name 5-amino-1-(5-phospho-D-ribosyl)imidazole formate-lyase . This enzyme catalyses the following chemical reaction

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:

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FeMoco (FeMo cofactor) is the primary cofactor of nitrogenase. Nitrogenase is the enzyme that catalyzes the conversion of atmospheric nitrogen molecules N2 into ammonia (NH3) through the process known as nitrogen fixation. Studying FeMoco's role in the reaction mechanism for nitrogen fixation is a potential use case for quantum computers. Even limited quantum computers could enable better simulations of the reaction mechanism.

<span class="mw-page-title-main">Aldehyde ferredoxin oxidoreductase</span>

In enzymology, an aldehyde ferredoxin oxidoreductase (EC 1.2.7.5) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Squire Booker</span> American biochemist

Squire Booker is an American biochemist at Penn State University. Booker directs an interdisciplinary chemistry research program related to fields of biochemistry, enzymology, protein chemistry, natural product biosynthesis, and mechanisms of radical dependent enzymes. He is an associate editor for the American Chemical Society Biochemistry Journal, is a Hughes Medical Institute Investigator, and an Eberly Distinguished Chair in Science at Penn State University.

In enzymology, a formylmethanofuran dehydrogenase (EC 1.2.99.5) is an enzyme that catalyzes the chemical reaction:

Methylthiotransferases are enzymes of the radical S-adenosyl methionine superfamily. These enzymes catalyze the addition of a methylthio group to various biochemical compounds including tRNA and proteins. Methylthiotransferases are classified into one of four classes based on their substrates and mechanisms. All methylthiotransferases have been shown to contain two Fe-S clusters, one canonical cluster and one auxiliary cluster, that both function in the addition of the methylthio group to the substrate.

References

  1. ↑ McLaughlin MI, Lanz ND, Goldman PJ, Lee KH, Booker SJ, Drennan CL (August 2016). "Crystallographic snapshots of sulfur insertion by lipoyl synthase". Proceedings of the National Academy of Sciences of the United States of America. 113 (34): 9446–50. doi: 10.1073/pnas.1602486113 . PMC   5003258 . PMID   27506792.
  2. ↑ Bank, RCSB Protein Data. "RCSB PDB - 5EXI: Crystal structure of M. tuberculosis lipoyl synthase at 2.28 A resolution". www.rcsb.org. Retrieved 2023-05-10.
  3. ↑ Jarrett JT (February 2015). "The biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical S-adenosylmethionine enzymes". The Journal of Biological Chemistry. 290 (7): 3972–9. doi: 10.1074/jbc.R114.599308 . PMC   4326807 . PMID   25477512.
  4. ↑ "InterPro". www.ebi.ac.uk. Retrieved 2020-04-20.
  5. ↑ Della Croce C, Bronzetti G, Cini M, Caltavuturo L, Poi G (2003-10-01). "Protective effect of lipoic acid against hydrogen peroxide in yeast cells". Toxicology in Vitro. Twelfth International Workshop on In vitro Toxicology. 17 (5–6): 753–9. doi:10.1016/j.tiv.2003.06.001. PMID   14599473.
  6. ↑ "Lipoic Acid". Linus Pauling Institute. 2014-04-28. Retrieved 2020-04-20.
  7. ↑ Zou J, Qi Q, Katavic V, Marillia EF, Taylor DC (December 1999). "Effects of antisense repression of an Arabidopsis thaliana pyruvate dehydrogenase kinase cDNA on plant development". Plant Molecular Biology. 41 (6): 837–49. doi:10.1023/a:1006393726018. OCLC   672002645. PMID   10737148. S2CID   8099883.
  8. ↑ Martins-Noguerol R, Moreno-Pérez AJ, Sebastien A, Troncoso-Ponce MA, Garcés R, Thomasset B, et al. (February 2020). "Impact of sunflower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants". Scientific Reports. 10 (1): 3749. Bibcode:2020NatSR..10.3749M. doi:10.1038/s41598-020-60686-z. PMC   7048873 . PMID   32111914.
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