Sugar biosynthesis, reaction mechanism

Detailed Reaction Mechanism of Deoxy Sugar Biosynthesis... 

The condensation step is catalyzed by the glycosyltransferase SpcF. Further enzyme-catalyzed oxidation is probably needed for the introduction of the hemiketal linkage between cyclitol and sugar units. The SpcY enzyme, which has a similar counterpart, HygY, among the /lyg-cluster encoded proteins (see Section 2.2.4.3.1), is a candidate enzyme for this reaction. SpcY is a member of the radical SAM superfamily of proteins and relatives of SpcY have been found before all in connection with molybdenum-cofactor biosynthesis but to our knowledge no details of the mechanism involved is known for those. 

A similar situation exists in the case of fatty acid synthesis, which proceeds from acetyl-CoA and reverses fatty acid breakdown. However, both carbon dioxide and ATP, a source of energy, are needed in the synthetic pathway. Furthermore, while oxidation of fatty acids requires NAD+ as one of the oxidants, and generates NADH, the biosynthetic process often requires the related NADPH. These patterns seen in biosynthesis of sugars and fatty acids are typical. Synthetic reactions resemble the catabolic sequences in reverse, but distinct differences are evident. These can usually be related to the requirement for energy and often also to control mechanisms. 

Methyl transfer reactions play a significant part in the modifications of aromatic polyketides, both of the polyketide core [61,62] as well as of several of the sugar moieties [44,53]. In Streptomyces, more than 20 amino acid sequences have been found that may represent enzymes involved in methyl transfer reactions in the biosynthesis of aromatic polyketides [149]. One of these enzymes, the S-adenosyl-L-methionine-dependent DnrK, is involved in the methylation of the C-4 hydroxyl group in daunorubicin/doxorubicin biosynthesis (Scheme 10, step 12). The subunit of the homo-dimeric enzyme displays a fold typical for small-molecule methyltransferases. The structure of the ternary complex with bound products S-adenosyl-L-homocysteine and 4-methoxy-8-rhodomycin provided insights into the structural basis of substrate recognition and catalysis [149]. The position and orientation of the substrates suggest an Sn2 mechanism for methyl transfer, and mutagenesis experiments show that there is no catalytic base in the vicinity of the substrate. Rate enhancement is thus most likely due to orientational and proximity effects [149]. 

A peculiar sugar modification occurs in the biosynthesis of the aclacino-mycins. These anthracyclines contain a trisaccharide moiety attached to the aklavinone scaffold at the C-7 position (Scheme 1). The first two carbohydrates in the aclacinomycins are rhodosamine and 2-deoxyfucose, but they differ structurally in their third sugar component, which is rhodinose in AclN, cinerulose A in AclA, L-aculose in AclY and cinerulose B in AclB [157]. The conversion of rhodinose to L-aculose is catalysed in a two-step process by the FAD-dependent enzyme aclacinomycin oxidoreductase [71] (Scheme 5, step 31). The three-dimensional structure of this oxidase revealed that the cofactor FAD is bound via two covalent bonds to the enzyme. Crystal structure and functional data further established a mechanism where the two different reactions are catalysed in the same active site of the enzyme but by different active site residues [71]. 

A wide variety of sugar alcohols have been found in plant material (see Chapter V). However, not much is known about the biosynthesis of these compounds. Because the alcohols generally occur together with the structurally related sugars, it has been assumed that mechanisms are available for interconverting them. The following reaction 80), found to occur in animal tissue, may occur in plants ... 

CMP-N-acetylneuraminic acid is formed by a series of reactions which are outgrowths of the pathways of hexosamine biosynthesis. As seen from Fig. 8A, N-acetylmannosamine can be regarded as the first specific intermediate in the biosynthesis of the nucleotide sugar and may be formed by 2-epimerization from either UDP-N-acetylglucosamine or N-acetylglucosamine. The mechanisms of these two reactions have recently been investigated and will be discussed below. 

Both L- and D-ribose occur in this complex mixture, but are not particularly abundant. Since all carbohydrates have somewhat similar chemical properties, it is difficult to envision simple mechanisms that could lead to the enrichment of ribose from this mixture, or how the relative yield of ribose required for the formation of RNA could be enhanced. However, the recognition that the biosynthesis of sugars leads not to the formation of free carbohydrates but of sugar phosphates, lead Albert Eschenmoser and his associates to show that under slightly basic conditions the condensation of glycoaldehyde-2-phosphate in the presence of formaldehyde considerable selectivity exist in the synthesis of ribose-2,4-diphosphate 54). This reaction has also been shown to take place under neutral conditions and low concentrations in the presence of minerals (55), and is particularly attractive given the properties of pyranosyl-RNA (p-RNA), a 2 ,4 -linked nucleic acid analogue whose backbone includes the six-member pyranose form of ribose-2,4-diphosphate 56). 

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