(acyl-carrier-protein) S-malonyltransferase

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Malonyl-CoA:ACP Transacylase
Identifiers
EC no. 2.3.1.39
CAS no. 37257-17-3
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In enzymology, a [acyl-carrier-protein] S-malonyltransferase (EC 2.3.1.39) is an enzyme that catalyzes the chemical reaction

Contents

malonyl-CoA + acyl carrier protein CoA + malonyl-[acyl-carrier-protein]

Thus, the two substrates of this enzyme are malonyl-CoA and acyl carrier protein, whereas its two products are CoA and malonyl-acyl-carrier-protein. This enzyme belongs to the family of transferases, specifically those acyltransferases transferring groups other than aminoacyl groups. This enzyme participates in fatty acid biosynthesis.

Nomenclature

The systematic name of this enzyme class is malonyl-CoA:[acyl-carrier-protein] S-malonyltransferase. Other names in common use include malonyl coenzyme A-acyl carrier protein transacylase,

Structure

Crystal Structures of FabD from E.coli [1] and Streptomyces coelicolor [2] are known and provide great insight into the catalytic mechanism of FabD. In E.Coli, FabD primarily involved in FAS pathway. However, in Streptomyces coelicolor, FabD is involved in FAS and polyketide synthase pathways. In both cases, the structures and active sites are very similar.

The crystal structure of (acyl-carrier-protein) S-malonyltransferase (FabD) in E.Coli [1] It is refined at 1.5A resolution to an R factor of 0.19l. The active site is shown in the form of a mesh grid.

The protein has an α/β type architecture, but the fold is unique. the active site inferred from the location of the catalytic Ser92 contains a typical nucleophilic elbow as observed in α/ β hydrolases. [1] Serine 92 is hydrogen bonded to His 201 in a fashion similar to various serine hydrolases. however, instead of the carboxylic acid typically found in catalytic triads, the main chain carbonyl of Gln 250 serves as a hydrogen bond acceptor in an interaction with His 201. [1] Two other residues, Arg-117 and Glu-11 are also located in the active site, but their function is not clear.

Function

The fatty acid synthetic pathway is the principal route for the production of membrane phospholipid acyl chains in bacterial and plants. [3] The reaction sequence is carried out by a series of individual soluble proteins that are each encoded by a discrete gene, and the pathway intermediates are shuttled between the enzymes. [3] Malony-CoA:ACP Transacylase (FabD) is one such individual soluble protein and catalyzes the following reaction:

malonyl-CoA + acyl carrier protein CoA + malonyl-[acyl-carrier-protein]

The transfer of malonate to acyl-carrier-protein (ACP) converts the acyl groups into thioester forms which are characteristic of acyl intermediates in fatty acid synthesis and which are strictly required for the condensation reactions catalyzed by β-ketoacyl-ACP synthetase. [4]

Mechanism

Malonyl-CoA:ACP Transacylase uses a ping-pong kinetic mechanism with a bound malonyl ester as the acyl intermediate attached to a serine residue residing within a GHSLG pentapeptide. [5] FabD first binds malonyl-CoA, the malonyl moiety is then transferred to the active siteSer 92, and CoA is released from the enzyme. ACP then binds and the malonyl moiety is transferred to the terminal sulfhydryl of the ACP prosthetic group. This reaction is readily reversible. [3] [6]

FabD reaction occurs via a ping-pong mechanism. In this first step, malonate is transferred from malonyl-coA to Ser 92 in the active site. His201 plays a role in activating Ser92 for nucleophilic attack on the incoming thioester. The CoA-SH functional group is then released from the enzyme and followed by ACP binding FabD Mechanism Step 1.tif
FabD reaction occurs via a ping-pong mechanism. In this first step, malonate is transferred from malonyl-coA to Ser 92 in the active site. His201 plays a role in activating Ser92 for nucleophilic attack on the incoming thioester. The CoA-SH functional group is then released from the enzyme and followed by ACP binding
His201 activates the thiol of ACP for nucleophilic attack on the malonyl-Ser92 intermediate (generated in the previous step), promoting its transfer to the thiol of ACP FabD Mechanism Step 2.tif
His201 activates the thiol of ACP for nucleophilic attack on the malonyl-Ser92 intermediate (generated in the previous step), promoting its transfer to the thiol of ACP

Industrial relevance

Among all known metabolic pathways in living systems, fatty acid biosynthesis yields the most energy dense products. [7] As a result, microbial fatty acid derivatives are emerging as a promising renewable energy alternative to fossil fuel derived transportation fuels. Recently, Khosla et al. [7] have devised a procedure to reconstitute E.Coli Fatty Acid Synthase using purified protein components (including FabD) and reported a detailed kinetic analysis of this in-vitro reconstituted system. [8] Their finding provide a new basis for assessing the scope and limitations of using E.Coli as a biocatalyst for the production of diesel fuels.

Clinical relevance

FabD as a target for Antibacterial Drug Discovery: An upcoming field

Fatty acid biosynthesis is carried out by the ubiquitous Fatty Acid Synthase. [9] Fatty acid synthase pathways are divided into two distinct molecular forms: Type I and Type II. [10] In Type I, Fatty Acid Synthase (found in humans and other mammals) is a single large polypeptide composed of several distinct domains. [11] On the other hand, each enzymatic activity (Condensation reaction, Reduction Reaction, Dehydration reaction) is found as a discrete protein in type II systems. [12] The difference in active site organization and predominance of type II FAS systems in bacteria make the enzymes of this pathway attractive targets for antibacterials. [9] [12]

FabD (Acyl-Carrier-Protein S-Malonyltransferase) is a reasonable target given that a high resolution crystal structure is available. [9] However, no FabD inhibitors have been reported in the literature and review articles on this topic. [9] The simple structure and acidity of malonate seem to permit few approaches to synthesizing derivatives (acting as potential inhibitors) that retain the character of the molecule.

A second approach for using FabD as a drug target is frequently identified in the literature: FabD can provide a useful tag for locating fab genes because FabD gene is usually adjacent to at least one other fab gene. [13] However (as of 2015), no potential drugs have attempted to exploit this feature.

Related Research Articles

<span class="mw-page-title-main">Coenzyme A</span> Coenzyme, notable for its synthesis and oxidation role

Coenzyme A (CoA, SHCoA, CoASH) is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle. All genomes sequenced to date encode enzymes that use coenzyme A as a substrate, and around 4% of cellular enzymes use it (or a thioester) as a substrate. In humans, CoA biosynthesis requires cysteine, pantothenate (vitamin B5), and adenosine triphosphate (ATP).

<span class="mw-page-title-main">Malonyl-CoA</span> Chemical compound

Malonyl-CoA is a coenzyme A derivative of malonic acid.

<span class="mw-page-title-main">Acyl carrier protein</span> Cofactor of both fatty acid and polyketide biosynthesis

The acyl carrier protein (ACP) is a cofactor of both fatty acid and polyketide biosynthesis machinery. It is one of the most abundant proteins in cells of E. coli. In both cases, the growing chain is bound to the ACP via a thioester derived from the distal thiol of a 4'-phosphopantetheine moiety.

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. In addition to cytosolic fatty acid synthesis, there is also mitochondrial fatty acid synthesis (mtFASII), in which malonyl-CoA is formed from malonic acid with the help of malonyl-CoA synthetase (ACSF3), which then becomes the final product octanoyl-ACP (C8) via further intermediate steps.

<span class="mw-page-title-main">Beta-ketoacyl-ACP synthase</span> Enzyme

In molecular biology, Beta-ketoacyl-ACP synthase EC 2.3.1.41, is an enzyme involved in fatty acid synthesis. It typically uses malonyl-CoA as a carbon source to elongate ACP-bound acyl species, resulting in the formation of ACP-bound β-ketoacyl species such as acetoacetyl-ACP.

<span class="mw-page-title-main">Biosynthesis of doxorubicin</span>

Doxorubicin (DXR) is a 14-hydroxylated version of daunorubicin, the immediate precursor of DXR in its biosynthetic pathway. Daunorubicin is more abundantly found as a natural product because it is produced by a number of different wild type strains of streptomyces. In contrast, only one known non-wild type species, streptomyces peucetius subspecies caesius ATCC 27952, was initially found to be capable of producing the more widely used doxorubicin. This strain was created by Arcamone et al. in 1969 by mutating a strain producing daunorubicin, but not DXR, at least in detectable quantities. Subsequently, Hutchinson's group showed that under special environmental conditions, or by the introduction of genetic modifications, other strains of streptomyces can produce doxorubicin. His group has also cloned many of the genes required for DXR production, although not all of them have been fully characterized. In 1996, Strohl's group discovered, isolated and characterized dox A, the gene encoding the enzyme that converts daunorubicin into DXR. By 1999, they produced recombinant Dox A, a Cytochrome P450 oxidase, and found that it catalyzes multiple steps in DXR biosynthesis, including steps leading to daunorubicin. This was significant because it became clear that all daunorubicin producing strains have the necessary genes to produce DXR, the much more therapeutically important of the two. Hutchinson's group went on to develop methods to improve the yield of DXR, from the fermentation process used in its commercial production, not only by introducing Dox A encoding plasmids, but also by introducing mutations to deactivate enzymes that shunt DXR precursors to less useful products, for example baumycin-like glycosides. Some triple mutants, that also over-expressed Dox A, were able to double the yield of DXR. This is of more than academic interest because at that time DXR cost about $1.37 million per kg and current production in 1999 was 225 kg per annum. More efficient production techniques have brought the price down to $1.1 million per kg for the non-liposomal formulation. Although DXR can be produced semi-synthetically from daunorubicin, the process involves electrophilic bromination and multiple steps and the yield is poor. Since daunorubicin is produced by fermentation, it would be ideal if the bacteria could complete DXR synthesis more effectively.

The enzyme [acyl-carrier-protein] phosphodiesterase (EC 3.1.4.14) catalyzes the reaction

In enzymology, a [acyl-carrier-protein] S-acetyltransferase is an enzyme that catalyzes the reversible chemical reaction

In enzymology, a beta-ketoacyl-acyl-carrier-protein synthase I is an enzyme that catalyzes the chemical reaction

In enzymology, a beta-ketoacyl-acyl-carrier-protein synthase II (EC 2.3.1.179) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Beta-ketoacyl-ACP synthase III</span> Enzyme

In enzymology, a β-ketoacyl-[acyl-carrier-protein] synthase III (EC 2.3.1.180) is an enzyme that catalyzes the chemical reaction

In enzymology, an erythronolide synthase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Fatty-acyl-CoA synthase</span>

Fatty-acyl-CoA Synthase, or more commonly known as yeast fatty acid synthase, is an enzyme complex responsible for fatty acid biosynthesis, and is of Type I Fatty Acid Synthesis (FAS). Yeast fatty acid synthase plays a pivotal role in fatty acid synthesis. It is a 2.6 MDa barrel shaped complex and is composed of two, unique multi-functional subunits: alpha and beta. Together, the alpha and beta units are arranged in an α6β6 structure. The catalytic activities of this enzyme complex involves a coordination system of enzymatic reactions between the alpha and beta subunits. The enzyme complex therefore consists of six functional centers for fatty acid synthesis.

<span class="mw-page-title-main">Holo-(acyl-carrier-protein) synthase</span>

In enzymology and molecular biology, a holo-[acyl-carrier-protein] synthase is an enzyme that catalyzes the chemical reaction:

<span class="mw-page-title-main">MCAT (gene)</span> Protein-coding gene in the species Homo sapiens

Malonyl CoA-acyl carrier protein transacylase, mitochondrial is an enzyme that in humans is encoded by the MCAT gene.

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

Germicidins are a groups of natural products arising from Streptomyces species that acts as autoregulatory inhibitor of spore germination. In Streptomyces viriochromogenes, low concentrations inhibit germination of its own arthrospores, and higher concentrations inhibit porcine Na+/K+ -activated ATPase. Inhibitory effects on germination are also observed when germicidin from Streptomyces is applied to Lepidium sativum. Germicidins and other natural products present potential use as pharmaceuticals, and in this case, those with possible antibiotic or antifungal activity.

Very-long-chain 3-oxoacyl-CoA synthase (EC 2.3.1.199, very-long-chain 3-ketoacyl-CoA synthase, very-long-chain beta-ketoacyl-CoA synthase, condensing enzyme, CUT1, CER6, FAE1, KCS, ELO) is an enzyme with systematic name malonyl-CoA:very-long-chain acyl-CoA malonyltransferase (decarboxylating and thioester-hydrolysing). This enzyme catalyses the following chemical reaction

3-hydroxydecanoyl-(acyl-carrier-protein) dehydratase (EC 4.2.1.60, D-3-hydroxydecanoyl-[acyl-carrier protein] dehydratase, 3-hydroxydecanoyl-acyl carrier protein dehydrase, 3-hydroxydecanoyl-acyl carrier protein dehydratase, β-hydroxydecanoyl thioester dehydrase, β-hydroxydecanoate dehydrase, beta-hydroxydecanoyl thiol ester dehydrase, FabA, β-hydroxyacyl-acyl carrier protein dehydratase, HDDase, β-hydroxyacyl-ACP dehydrase, (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] hydro-lyase) is an enzyme with systematic name (3R)-3-hydroxydecanoyl-(acyl-carrier protein) hydro-lyase. This enzyme catalyses the following chemical reaction

<span class="mw-page-title-main">Ketoacyl synthase</span> Catalyst for a key step in fatty acid synthesis

Ketoacyl synthases (KSs) catalyze the condensation reaction of acyl-CoA or acyl-acyl ACP with malonyl-CoA to form 3-ketoacyl-CoA or with malonyl-ACP to form 3-ketoacyl-ACP. This reaction is a key step in the fatty acid synthesis cycle, as the resulting acyl chain is two carbon atoms longer than before. KSs exist as individual enzymes, as they do in type II fatty acid synthesis and type II polyketide synthesis, or as domains in large multidomain enzymes, such as type I fatty acid synthases (FASs) and polyketide synthases (PKSs). KSs are divided into five families: KS1, KS2, KS3, KS4, and KS5.

Elongase is a generic term for an enzyme that extends the length of fatty acid. The nomenclature is not applied rigorously. Often, elongase refers to enzymes that produce very long chain fatty acids. Sometimes, elongase also includes unsaturases, which introduce C=C double bonds in the backbone. Because fatty acids and their derivatives are biochemically influential, elongases are of considerable interest.

References

  1. 1 2 3 4 Serre L, Verbree EC, Dauter Z, Stuitje AR, Derewenda ZS (Jun 1995). "The Escherichia coli malonyl-CoA:acyl carrier protein transacylase at 1.5-A resolution. Crystal structure of a fatty acid synthase component". The Journal of Biological Chemistry. 270 (22): 12961–4. doi: 10.1074/jbc.270.22.12961 . PMID   7768883.
  2. Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJ, O'Connell JD, Khosla C, Stroud RM (Feb 2003). "Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase". Structure. 11 (2): 147–54. doi: 10.1016/s0969-2126(03)00004-2 . PMID   12575934.
  3. 1 2 3 4 White SW, Zheng J, Zhang YM (Jun 2005). "The structural biology of type II fatty acid biosynthesis". Annual Review of Biochemistry. 74 (1): 791–831. doi:10.1146/annurev.biochem.74.082803.133524. PMID   15952903.
  4. Ruch FE, Vagelos PR (Dec 1973). "The isolation and general properties of Escherichia coli malonyl coenzyme A-acyl carrier protein transacylase". The Journal of Biological Chemistry. 248 (23): 8086–94. doi: 10.1016/S0021-9258(19)43197-9 . PMID   4584822.
  5. Ruch FE, Vagelos PR (Dec 1973). "The isolation and general properties of Escherichia coli malonyl coenzyme A-acyl carrier protein transacylase". The Journal of Biological Chemistry. 248 (23): 8086–94. doi: 10.1016/S0021-9258(19)43197-9 . PMID   4584822.
  6. Oefner C, Schulz H, D'Arcy A, Dale GE (Jun 2006). "Mapping the active site of Escherichia coli malonyl-CoA-acyl carrier protein transacylase (FabD) by protein crystallography". Acta Crystallographica Section D. 62 (Pt 6): 613–618. doi:10.1107/S0907444906009474. PMID   16699188.
  7. 1 2 Liu T, Khosla C (2010). "Genetic engineering of Escherichia coli for biofuel production". Annual Review of Genetics. 44: 53–69. doi:10.1146/annurev-genet-102209-163440. PMID   20822440.
  8. Yu X, Liu T, Zhu F, Khosla C (Nov 2011). "In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli". Proceedings of the National Academy of Sciences of the United States of America. 108 (46): 18643–8. Bibcode:2011PNAS..10818643Y. doi: 10.1073/pnas.1110852108 . PMC   3219124 . PMID   22042840.
  9. 1 2 3 4 Payne DJ, Warren PV, Holmes DJ, Ji Y, Lonsdale JT (May 2001). "Bacterial fatty-acid biosynthesis: a genomics-driven target for antibacterial drug discovery". Drug Discovery Today. 6 (10): 537–544. doi:10.1016/S1359-6446(01)01774-3. PMID   11369293.
  10. Rock CO, Cronan JE (Jul 1996). "Escherichia coli as a model for the regulation of dissociable (type II) fatty acid biosynthesis". Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism. 1302 (1): 1–16. doi:10.1016/0005-2760(96)00056-2. PMID   8695652.
  11. Chirala SS, Huang WY, Jayakumar A, Sakai K, Wakil SJ (May 1997). "Animal fatty acid synthase: functional mapping and cloning and expression of the domain I constituent activities". Proceedings of the National Academy of Sciences of the United States of America. 94 (11): 5588–93. Bibcode:1997PNAS...94.5588C. doi: 10.1073/pnas.94.11.5588 . PMC   20822 . PMID   9159116.
  12. 1 2 Tsay JT, Oh W, Larson TJ, Jackowski S, Rock CO (Apr 1992). "Isolation and characterization of the beta-ketoacyl-acyl carrier protein synthase III gene (fabH) from Escherichia coli K-12". The Journal of Biological Chemistry. 267 (10): 6807–14. doi: 10.1016/S0021-9258(19)50498-7 . PMID   1551888.
  13. Campbell JW, Cronan JE (2001). "Bacterial fatty acid biosynthesis: targets for antibacterial drug discovery". Annual Review of Microbiology. 55: 305–32. doi:10.1146/annurev.micro.55.1.305. PMID   11544358.

Further reading