Amide-bound acyl groups

A similar distribution of fatty acids has also been detected in lipid A of other bacteria (Fig. 5). Thus, in Fusobacterium nucleatum, 2 moles of (R)-3-OH-14 0 are ester-bound, one of which is 3-O-acylated by 14 0. In amide linkage, (R)-3-0(14 0)-16 0 is present. In Vibrio cholerae, a dimer of (R)-3-OH-12 0 is bound as an ester while (R)-3-0-(14 0)-14 0 and (R)-3-0-(16 0)-14 0 are amide-linked. The lipid A component of Chromobacterium violaceum possesses 2 moles of (R)-3-OH-10 0 in ester linkage. The amide-bound acyl groups are represented by (R)-3-0H-12 0 residues which are 3-0-acylated by 12 0 and (S)-2-OH-12 0. In P. mirabilis, 3-0H-14 0 is, like in Salmonella, ester-and amide-bound. In this case, however, exclusively 14 0 substitutes the 3-hydroxyl groups of both 0- and N-linked 3-OH-14 0. 

Figure 5. Ester- and amide-bound acyl groups present in lipid As of different bacterial...

The crystal structure of a CODH/ACS enzyme was reported only in 2002.43,44 It reveals a trio of Fe, Ni, and Cu at the active site (6). The Cu is linked to the Ni atom through two cysteine-S, the Ni being square planar with two terminal amide ligands. Planarity and amide coordination bear some resemblance to the Ni porphinoid in MCR. A two-metal ion mechanism is likely for acetyl CoA synthesis, in which a Ni-bound methyl group attacks an adjacent Cu—CO fragment with formation of a Cu-acyl intermediate. A methylnickel species in CODH/ACS has been identified by resonance Raman spectroscopy.45... 

Owing to the acyl group to which it is bound, the amino-group loses its basic character almost entirely. Salts of the amides with strong acids are indeed known, but such salts are immediately and completely decomposed into their constituents by water. Only urea, the diamide of carbonic acid, forms stable salts, the existence of which is made possible by the second NHa-group. 

Poor nucleophiles react with acyl isoureas B so slowly that the latter start to decompose. In some sense they acylate themselves. The N atom designated with the positional number 3 intramolecularly substitutes the O-bound leaving group that is attached to the carboxyl carbon Cl. A four-membered cyclic tetrahedral intermediate is formed. When the Cl -Ol bond in this intermediate opens up, the N-acyl urea E is produced. Because compound E is an amide derivative it is no longer an acylating agent (cf. Section 6.2). 

The Af-acyl groups in bound proline and hydroxyproline differ from all the other peptide groups in being fully substituted tertiary amides. Whereas secondary peptides (XXXIX) may form anions (XXXX) by abstraction of a proton from the nitrogen atom, the formation of an anion (XXXXII) from a proline peptide (XXXXI) would have to proceed with cleavage of... 

The two steps are explained by the formation of a covalently bound enzyme- substrate intermediate (Figure 9,5). First, the acyl group of the substrate becomes covalently attached to the enzyme as p-nitrophenolate (or an amine if the substrate is an amide rather than an ester) is released. The enzyme-acyl group complex is called the acyl-enzyme intermediate. Second, the acyl-eni yme intermediate is hydrolyzed to release the carboxylic acid component of t ie substrate and regenerate the free enzyme. Thus, one molecule of p-nitrophenolate is produced rapidly from each enzyme molecule as the acyl-enzyme intermediate is formed. However, it takes longer for the enzyme to he reset by the hydrolysis of the acyl-enzyme intermediate, both steps are required for enzyme turnover. 

All cases discussed in this section involve the reaction between an amine and an acyl group to yield an amide. The high-energy cofactor required is in most cases an acyl-coenzyme A derivative (acyl-S-CoA) where the acyl moiety is bound by a thioester linkage. 

Primary cultures of neurons, but not astrocytes, contain detectable quantities of a lipid component which we have identified as NAPE by enzymatic cleavage, multiple chromatographic analyses and nuclear magnetic resonance spectroscopy. Neuronal NAPE is composed of a variety of molecular species, which differ in the fatty acyl group bound, through an amide bond, to the ethanolamine moiety of phosphatidylethanolamine (PE). We have found at least five such molecular species in cultured neurons (Table 6.1). 

Piperazine-2,5-diones can be symmetric or asymmetric. Symmetric DKPs are readily obtained by heating amino acid esters,1179-181 whereas asymmetric DKPs are obtained directly from the related dipeptides under basic or, more properly, acid catalysis, or by cyclocondensation of dipeptide esters.1182-185 As an alternative procedure hexafluoroacetone can be used to protect/activate the amino acid for the synthesis of symmetric DKPs or of the second amino acid residue for synthesis of the dipeptide ester and subsequent direct cyclocondensation to DKPs.1186 The use of active esters for the cyclocondensation is less appropriate since it may lead to epimerization when a chiral amino acid is involved as the carboxy component in the cyclization reaction. Resin-bound DKPs as scaffolds for further on-resin transformations are readily prepared using the backbone amide linker (BAL) approach, where the amino acid ester is attached to the BAL resin by its a-amino group and then acylated with a Fmoc-protected amino acid by the HATU procedure, N -deprotection leads to on-resin DKP formation1172 (see Section 6.8.3.2.2.3). 

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