Enzymes synthase

Lipases are enzymes that catalyze the in vivo hydrolysis of lipids such as triacylglycerols. Lipases are not used in biological systems for ester synthesis, presumably because the large amounts of water present preclude ester formation due to the law of mass action which favors hydrolysis. A different pathway (using the coenzyme A thioester of a carboxylic acid and the enzyme synthase [Blei and Odian, 2000]) is present in biological systems for ester formation. However, lipases do catalyze the in vitro esterification reaction and have been used to synthesize polyesters. The reaction between alcohols and carboxylic acids occurs in organic solvents where the absence of water favors esterification. However, water is a by-product and must be removed efficiently to maximize conversions and molecular weights. 

Aminoacylation assays have revealed that overexpressed peptide synthetases are only incompletely pusttranslationally modified by pantetheine. Tyrocidine synthetase 1 expressed in E. coJi contains about 1.5% holo-enzyme (80). The reduced cofactitr content leads to decreased activities in aminoacylation and epimerization reactions, which require the cofactor (64,80,84)- Some evidence has been obtained that apo-eniymes may slightly differ from holo--en2ymes with respect to catalytic properties (80). Addition of 4 -phos-phopantetheine is thought to be catalyzed by a holo-enzyme synthase utilizing CoA ... 

As foreshadowed in Chapter 8, Scheme 8.70, it is now clear that in many species, fatty acids (and as will become apparent later, polyketide antibiotics and related materials) are derived from acetyl-CoA and, occasionally, other starter CoA (pro-panoyl,butryl, etc.) units. Overall, and in a most general sense, the assembly of fatty acids and related compounds on a polyketide synthase (PKS) enzyme begins with an acetyl (or related) starter unit (as abbreviated in Scheme 11.34) transferred to the synthase enzyme from an acetyl-CoA (or related) species (Scheme 11.35). Once attached to the enzyme synthase complex, the addition of a two-carbon unit via (what appears to be) a Claisen-type condensation takes place with a malonyl... 

Figure C3.2.17. Diagram of a liposome-based artificial photosynthetic membrane showing the photocycle that pumps protons into the interior of the liposome and the CFqF j-ATP synthase enzyme. From [55],...

In the next step the —OOH group of PGG2 is reduced to an alcohol function Again prostaglandin endoperoxide synthase is the enzyme responsible The product of this step IS called PGH2... 

The enzyme system responsible for the biosynthesis of PGs is widely distributed in mammalian tissues and has been extensively studied (2). It is referred to as prostaglandin H synthase (PGHS) and exhibits both cyclooxygenase and peroxidase activity. In addition to the classical PGs two other prostanoid products, thromboxane [57576-52-0] (TxA ) (3) and prostacyclin [35121 -78-9] (PGI2) (4) are also derived from the action of the enzyme system on arachidonic acid (Fig. 1). 

In order for the cyclooxygenase to function, a source of hydroperoxide (R—O—O—H) appears to be required. The hydroperoxide oxidizes a heme prosthetic group at the peroxidase active site of PGH synthase. This in turn leads to the oxidation of a tyrosine residue producing a tyrosine radical which is apparendy involved in the abstraction of the 13-pro-(5)-hydrogen of AA (25). The cyclooxygenase is inactivated during catalysis by the nonproductive breakdown of an active enzyme intermediate. This suicide inactivation occurs, on average, every 1400 catalytic turnovers. 

Fohc acid is a precursor of several important enzyme cofactors required for the synthesis of nucleic acids (qv) and the metaboHsm of certain amino acids. Fohc acid deficiency results in an inabiUty to produce deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and certain proteins (qv). Megaloblastic anemia is a common symptom of folate deficiency owing to rapid red blood cell turnover and the high metaboHc requirement of hematopoietic tissue. One of the clinical signs of acute folate deficiency includes a red and painhil tongue. Vitamin B 2 folate share a common metaboHc pathway, the methionine synthase reaction. Therefore a differential diagnosis is required to measure foHc acid deficiency because both foHc acid and vitamin B 2 deficiency cause... 

The key enzyme in this sequence, isopenicillin N synthase (IPNS), has been purified from E. coli (59) and the recombinant enzyme shown to be a single polypeptide of 336 amino acids containing two cysteines, numbers 106 and 255 from the /V-teiminus, and probably a ferrous ion in a nonheme environment. The enzyme has been crystallized and studies undertaken to obtain suitably sized crystals for diffraction studies. 

Hydrolases represent a significant class of therapeutic enzymes [Enzyme Commission (EC) 3.1—3.11] (14) (Table 1). Another group of enzymes with pharmacological uses has budt-ia cofactors, eg, in the form of pyridoxal phosphate, flavin nucleotides, or zinc (15). The synthases, and other multisubstrate enzymes that require high energy phosphates, are seldom available for use as dmgs because the required co-substrates are either absent from the extracellular space or are present ia prohibitively low coaceatratioas. 

The final application considered in this chapter is chosen to illustrate the application of a QM-MM study of an enzyme reaction that employs an ab initio Hamiltonian in the quantum region [67]. Because of the computational intensity of such calculations there are currently very few examples in the literahire of QM-MM shidies that use a quanhim mechanical technique that is more sopliisticated than a semiempirical method. MuUiolland et al. [67] recently reported a study of part of the reaction catalyzed by citrate synthase (CS) in wliich the quanhim region is treated by Hartree-Fock and MP2 methods [10,51],... 

Figure 5 A suggested mechanism for the enolization of acetyl-CoA by the enzyme citrate synthase (CS). The keto, enolate, and enol forms of the substrate are shown.

The first sequence is from the enzyme citrate synthase, residues 260-270, which form a buried helix the second sequence is from the enzyme alcohol dehydrogenase, residues 355-365, which form a partially exposed helix and the third sequence is from troponin-C, residues 87-97, which form a completely exposed helix. Charged residues are colored red, polar residues ate blue, and hydrophobic residues are green. 

Figure 4.6 The bifunctional enzyme PRA-isomerase (PRAI) IGP-synthase (IGPS) catalyzes two sequential reactions in the biosynthesis of tryptophan. In the first reaction (top half), which is catalyzed by the C-terminal PRAI domain of the enzyme, the substrate N-(5 -phosphoribosyl) anthranilate (PRA) is converted to l-(o-carboxyphenylamino)-l-deoxyribulose 5-phosphate (CdRP) by a rearrangement reaction. The succeeding step (bottom half), a ring closure reaction from CdRP to indole-3-glycerol phosphate (IGP), is catalyzed by the N-terminal IGPS domain.

PRA-isomerase lGP-synthase, a bifunctional enzyme from E. coli that catalyzes two reactions in the synthesis of tryptophan (Figure 4.6), has a polypeptide chain that forms two a/p barrels. The stmcture of this enzyme, solved at 2.8 A in the laboratory of Hans Jansonius in Basel, Switzerland, showed that residues 48-254 form one barrel with IGP-synthase activity, while residues 255-450 form the second barrel with PRA-isomerase activity (Figure 4.7). 

Figure 4.7 Two of the enzymatic activities involved in the biosynthesis of tryptophan in E. coli, phosphoribosyl anthranilate (PRA) isomerase and indoleglycerol phosphate (IGP) synthase, are performed by two separate domains in the polypeptide chain of a bifunctional enzyme. Both these domains are a/p-barrel structures, oriented such that their active sites are on opposite sides of the molecule. The two catalytic reactions are therefore independent of each other. The diagram shows the IGP-synthase domain (residues 48-254) with dark colors and the PRA-isomerase domain with light colors. The a helices are sequentially labeled a-h in both barrel domains. Residue 255 (arrow) is the first residue of the second domain. (Adapted from J.P. Priestle et al., Proc.

Priestle, J.P, et al. Three-dimensional structure of the bifunctional enzyme N-(5 -phosphoribosyl) anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escheriehia eoli. Proc. Natl. Aead. 

Despite considerable efforts very few membrane proteins have yielded crystals that diffract x-rays to high resolution. In fact, only about a dozen such proteins are currently known, among which are porins (which are outer membrane proteins from bacteria), the enzymes cytochrome c oxidase and prostaglandin synthase, and the light-harvesting complexes and photosynthetic reaction centers involved in photosynthesis. In contrast, many other membrane proteins have yielded small crystals that diffract poorly, or not at all, using conventional x-ray sources. However, using the most advanced synchrotron sources (see Chapter 18) it is now possible to determine x-ray structures from protein crystals as small as 20 pm wide which will permit more membrane protein structures to be elucidated. 

Both threo- (14) and eo f >"4-fluoro-DL-glutamic acid (/5) are noncompetitive inhibitors of glutamine synthase, an enzyme that catalyzes the synthesis of glutamine from L-glutamic acid and ammonia. This mhibibon may explain the... 

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