Phosphopantetheine proteins

Spedfic details vary somewhat from spedes to spedes, but this scheme illustrates a typical phosphopantetheine protein involvement. 

Pantothenic acid, sometimes called vitamin B3, is a vitamin that makes up one part of a complex coenzyme called coenzyme A (CoA) (Figure 18.23). Pantothenic acid is also a constituent of acyl carrier proteins. Coenzyme A consists of 3, 5 -adenosine bisphosphate joined to 4-phosphopantetheine in a phosphoric anhydride linkage. Phosphopantetheine in turn consists of three parts /3-mercaptoethylamine linked to /3-alanine, which makes an amide bond with a branched-chain dihydroxy acid. As was the case for the nicotinamide and flavin coenzymes, the adenine nucleotide moiety of CoA acts as a recognition site, increasing the affinity and specificity of CoA binding to its enzymes. 

The 4-phosphopantetheine group of CoA is also utilized (for essentially the same purposes) in acyl carrier proteins (ACPs) involved in fatty acid biosynthesis (see Chapter 25). In acyl carrier proteins, the 4-phosphopantetheine is covalently linked to a serine hydroxyl group. Pantothenic acid is an essential factor for the metabolism of fat, protein, and carbohydrates in the tricarboxylic acid cycle and other pathways. In view of its universal importance in metabolism, it is surprising that pantothenic acid deficiencies are not a more serious problem in humans, but this vitamin is abundant in almost all foods, so that deficiencies are rarely observed. 

FIGURE 25.6 Fatty acids are conjugated both to coenzyme A and to acyl carrier protein through the sulfliydryl of phosphopantetheine prosthetic groups. 

In bacteria, ACP is a small protein of 77 residues that transports an acyl group from enzyme to enzyme. In vertebrates, however, ACP appears to be a long arm on a multienzyme synthase complex, whose apparent function is to shepherd an acyl group from site to site within the complex. As in acetyl CoA, the acyl group in acetyl ACP is linked by a thioester bond to the sulfur atom of phosphopantetheine. The phosphopantetheine is in turn linked to ACP through the side-chain -OH group of a serine residue in the enzyme. 

Figure 21-2. Fatty acid synthase multienzyme complex. The complex is a dimer of two identical polypeptide monomers, 1 and 2, each consisting of seven enzyme activities and the acyl carrier protein (ACP). (Cys— SH, cysteine thiol.) The— SH of the 4 -phosphopantetheine of one monomer is in close proximity to the— SH of the cysteine residue of the ketoacyl synthase of the other monomer, suggesting a "head-to-tail" arrangement of the two monomers. Though each monomer contains all the partial activities of the reaction sequence, the actual functional unit consists of one-half of one monomer interacting with the complementary half of the other. Thus, two acyl chains are produced simultaneously. The sequence of the enzymes in each monomer is based on Wakil.

Figure 11.2 Biosynthesis of the nine-membered enediynes. Members of this family share a common biosynthetic pathway for the enediyne core intermediate. Domains are shown in circles with abbreviations (KS, ketosynthase AT, acyltransferase KR, ketoreductase DH, dehydratase TE, thioesterase ACP, acyl carrier protein PPT, phosphopantetheine transferase)...

Earlier in this chapter, it was mentioned that many of the nonprotein amino acids are components of nonribosomal peptides. During such a biosynthesis, the peptide is attached to a carrier protein through a thioester bond, until chain termination occurs and the final product is released. The carrier protein is posttranslationally modified by the attachment of a phosphopantetheinyl group from coenzyme A. This step gives rise to the active carrier protein with a phosphopantetheine arm upon which amino acids are added to during NRPS. As an example, loading of isoleucine onto the carrier protein is depicted below (Scheme 5). Further details about nonribosomal peptide syntheses and enzymatic reactions can be found in Chapter 5.19. 

Scheme 5 Loading of isoleucine onto the phosphopantetheine arm of a carrier protein domain.

Some enzymes are nonfunctional until posttranslationally modified. Examples of these enzymes include the acyl- and carboxyltransferases. While lipoate and phosphopantetheine are necessary for acyl transfer chemistry, tethered biotin is used in carboxyl transfer chemistry. Biotin and lipoate tethering occur under a similar mechanism the natural small molecule is activated with ATP to form biotinyl-AMP or lipoyl-AMP (Scheme 20). A lysine from the target protein then attacks the activated acid and transfers the group to the protein. The phosphopantetheine moiety is transferred using its own enzyme, the phosphopantetheinyltrans-ferase (PPTase). The PPTase uses a nucleophilic hydroxy-containing amino acid, serine, to attach the phosphopantetheinyl (Ppant) arm found in coenzyme A to convert the apo (inactive) carrier protein to its holo (active) form. The reaction is Mg -dependent. 

Phosphopantetheine tethering is a posttranslational modification that takes place on the active site serine of carrier proteins - acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs), also termed thiolation (T) domains - during the biosynthesis of fatty acids (FAs) (use ACPs) (Scheme 23), polyketides (PKs) (use ACPs) (Scheme 24), and nonribosomal peptides (NRPs) (use T domain) (Scheme 25). It is only after the covalent attachment of the 20-A Ppant arm, required for facile transfer of the various building block constituents of the molecules to be formed, that the carrier proteins can interact with the other components of the different multi-modular assembly lines (fatty acid synthases (FASs), polyketide synthases (PKSs), and nonribosomal peptide synthetases (NRPSs)) on which the compounds of interest are assembled. The structural organizations of FASs, PKSs, and NRPSs are analogous and can be divided into three broad classes the types I, II, and III systems. Even though the role of the carrier proteins is the same in all systems, their mode of action differs from one system to another. In the type I systems the carrier proteins usually only interact in cis with domains to which they are physically attached, with the exception of the PPTases and external type II thioesterase (TEII) domains that act in trans. In the type II systems the carrier proteins selectively interact... 

The section of the molecule discussed so far represents a functional unit. In the cell, it is produced from pantothenate. The molecule also occurs in a protein-bound form as 4 -phosphopantetheine in the enzyme fatty acid synthase (see p. 168). In coenzyme A, however, it is bound to 3, 5 -adenosine diphosphate. 

This enzyme catalyzes the NADPH- and dioxygen-dependent insertion of cis double bonds into the methylene region of fatty acyl structures covalently attached to the phosphopantetheine portion of an acyl carrier protein. 

Pantothenic acid (vitamin B5) is both present in many nutrientcients and it is also produced by intestinal bacteria. Deficiency is therefore thought to be unlikely. Its active form, 4-phosphopantetheine, is an element of both coenzyme-A and acyl-carrier protein and thus participates in fatty acid synthesis and in the posttranslational modification of proteins. Acetylcoenzyme-A is important for the synthesis of the neurotransmitter acetylcholine. 

FIGURE 21-4 Acyl carrier protein (ACP). The prosthetic group is 4 -phosphopantetheine, which is covalently attached to the hydroxyl group of a Ser residue in ACP. Phosphopantetheine contains the B vitamin pantothenic acid, also found in the coenzyme A molecule. Its —SH group is the site of entry of malonyl groups during fatty acid synthesis. 

FIGURE 21-5 Sequence of events during synthesis of a fatty acid. The fatty acid synthase complex is shown schematically. Each segment of the disk represents one of the six enzymatic activities of the complex. At the center is acyl carrier protein (ACP), with its phosphopantetheine arm ending in an —SH. The enzyme shown in blue is the one that will act in the next step. As in Figure 21-3, the initial acetyl group is shaded yellow, C-1 and C-2 of malonate are shaded pink, and the carbon released as C02 is shaded green. Steps (T) to (7) are described in the text. 

The remaining series of reactions of fatty acid synthesis in eukary-l otes is catalyzed by the multifunctional, dimeric enzyme, fatty acid synthase. Each fatty acid synthase monomer is a multicatalytic polypeptide with seven different enzymic activities plus a domain that covalently binds a molecule of 4 -phosphopantetheine. [Note 4-Phosphopantetheine, a derivative of the vitamin pantothenic add (see p. 379), carries acetyl and acyl units on its terminal thiol (-SH)j group during fatty acid synthesis. It also is a component of 00-enzyme A.] In prokaryotes, fatty acid synthase is a multienzyme complex, and the 4 -phosphopantetheine domain is a separate protein, referred to as the acyl carrier protein (ACP). ACP is used below to refer to the phosphopantetheine-binding domain of the eukaryotic fatty acid synthase molecule. The reaction numbers in1 brackets below refer to Figure 16.9. [Note The enzyme activities listed are actually separate catalytic domains present in each mulf-1 catalytic fatty acid synthase monomer.]... 

Phosphopantetheine-containing active carriers Acyl carrier protein domain, coenzyme A Coenzyme A... 

Attachment of phosphopantetheine to proteins is catalyzed by a phosphotransferase that utilizes CoA as the donor. A phosphodiesterase removes the phosphopantetheine, providing a turnover cycle.15, 5b A variety of synthetic analogs have been made.4 16 The reactive center of CoA and phosphopantetheine is the SH group, which is carried on a flexible arm that consists in part of the (3-alanine portion of pantothenic acid. A mystery is why pantoic acid, a small odd-shaped molecule that the human body cannot make, is so essential for life. The hydroxyl group is a potential reactive site and the two methyl groups may enter into formation of a "trialkyl lock" (p. 485), part of a sophisticated "elbow" or shoulder for the SH-bearing arm. 

In higher animals as well as in My cobacterium,207 yeast,208 and Euglena, the fatty acid synthase consists of only one or two multifunctional proteins. The synthase from animal tissues has seven catalytic activities in a single 263-kDa 2500-residue protein 209 The protein consists of a series of domains that contain the various catalytic activities needed for the entire synthetic sequence. One domain contains an ACP-like site with a bound 4 -phosphopantetheine as well as a cysteine side chain in the second acylation site. This synthase produces free fatty acids, principally the C16 palmitate. The final step is cleavage of the acyl-CoA by a thioesterase, one of the seven enzymatic activities of the synthase. See Chapter 21 for further discussion. 

The soluble enzyme system responsible for its synthesis contains a large 280-kDa protein that not only activates the amino acids as aminoacyl adenylates and transfers them to thiol groups of 4 -phosphopantetheine groups covalently attached to the enzyme but also serves as a template for joining the amino acids in proper sequence.211-214 Four amino acids—proline, valine, ornithine (Om), and leucine—are all bound. 

Phosphopantetheine coenzymes are the biochemically active forms of the vitamin pantothenic acid. In figure 10.11, 4 -phosphopantetheine is shown as covalently linked to an adenylyl group in coenzyme A or it can also be linked to a protein such as a serine hydroxyl group in acyl carrier protein (ACP). It is also found bonded to proteins that catalyze the activation and polymerization of amino acids to polypeptide antibiotics. Coenzyme A was discovered, purified, and structurally characterized by Fritz Lipmann and colleagues in work for which Lipmann was awarded the Nobel Prize in 1953. 

One system in which pantetheine almost certainly performs such a carrier role is the fatty acid synthase from E. coli, in which 4 -phosphopantetheine is a component of the acyl carrier protein (see chapter 18). 

Fatty acid synthesis takes place in eight steps. All except the first step take place on a multienzyme complex. The intermediates on this complex are carried by attachment of the acid group in thioester linkage to phosphopantetheine of the acyl carrier protein (ACP). The multienzyme complex greatly increases the efficiency of fatty acid synthesis, because for each step in the pathway the next enzyme is always near at hand, and the dilution of intermediates is minimized. 

The synthetase consists of the three modules E1, E2, and E3 (for a complete description, see Sec. II. A). Each module is composed of an activation site forming the acyl or aminoacyl adenylate, a carrier domain which is posttranslationally modified with 4 -phosphopantetheine (Sp), and a condensation domain (Cl, C2) or, alternatively, a structurally similar epimerization domain (Ep). Activation of aminoadipate (Aad) leads to an acylated enzyme intermediate, in which Aad is attached to the terminal cysteamine of the cofactor (El-Spl-Aad) [reactions (1) and (2)]. Likewise, activation of cysteine (Cys) leads to cysteinylated module 2 [reactions (3) and (4)]. For the condensation reaction to occur between aminoadipate as donor and cysteine as acceptor, both intermediates are thought to react at the condensation site of module 1 (Cl). Each condensation site is composed, in analogy to ribosomal peptide formation, of an aminoacyl and a peptidyl site. In this case of initiation, the thioester of Aad enters the P-site, while the thioester of Cys enters the A-site. Condensation occurs and leaves the dipeptidyl intermediate Aad-Cys at the carrier protein of the second module [reaction (5)]. The third amino acid valine is activated on module 3, and Val is attached to the carrier protein 3 [reactions (6) and (7)]. Formation of the tripeptide occurs at the second condensation site C2, with the dipeptidyl intermediate entering the P-site and the valiny 1-intermediate the A-site [reaction (8)]. 

Phosphopantothenic acid reacts with cysteine, forming 4 -phosphopant-othenyl cysteine, which is decarboxylated to 4 -phosphopantetheine in a flavin-dependent reaction. In most bacteria, phosphopantetheinyl cysteine synthase and decarboxylase occur as a single bifunctional enzyme, but the human enzymes occur as two separate proteins (Daugherty et al., 2002). 

Phosphopantetheine undergoes adenylyl transfer from ATP to yield de-phospho-CoA, which is then phosphorylated at the 3 position of the ribose moiety to yield CoA. Phosphopantetheine adenylyltransferase and dephos-pho- CoA kinase activities occur in a single bifunctional enzyme, which is found in both cytosol and mitochondria. However, in addition to the bifunctional protein, human tissues also contain a separate dephospho-CoA kinase (Begley et al., 2001 Zhyvoloup et al., 2002). 

Phosphopantetheine, arising from either the catabolism of CoA or the inactivation of holo - acyl carrier protein (ACP), can be reutilized for CoA synthesis. Phosphopantetheine is a potent inhibitor of pantothenic acid kinase, the first step of de novo CoA synthesis. 

Polyketide synthases, fatty acid synthases, and non-ribosomal peptide synthetases are a structurally and mechanistically related class of enzymes that catalyze the synthesis of biopolymers in the absence of a nucleic acid or other template. These enzymes utilize the common mechanistic feature of activating monomers for condensation via covalently-bound thioesters of phosphopantetheine prosthetic groups. The information for the sequence and length of the resulting polymer appears to be encoded entirely within the responsible proteins. 

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