Biosynthetic enzymes functions

Yoganathan, A., Isolation, expression and functional analysis of a cDNA encoding phytoene desaturase, a carotenoid biosynthetic enzyme from rice, Oryza sativa L., PhD dissertation. Graduate School and University Center, City University of New York, 1998. 

The variation of the chemical structures in both Type I and Type II compounds results from differences in both biosynthetic enzyme systems and their starting material. This topic, however, has been judiciously described in the chapter by R. Jurenka. While the grouping employed in this chapter is based on biosynthetic origin, some chemicals were involuntarily classified considering their functional groups more sizably than the origin. Incidentally, taxonomic information is important for insect pheromone research. In this chapter, the family name (with the common suffix -idae) is associated with the species name. For those species whose family name is not listed in Figs. 1 and 2, the superfamily name (with the common suffix -oidea) is associated. The subfamily name (with the common suffix -inae) is also described for the species in Tor-tricidae, Pyralidae, and Noctuidae. 

The 3-ketothiolase has been purified and investigated from several poly(3HB)-synthesizing bacteria including Azotobacter beijerinckii [10], Ral-stonia eutropha [11], Zoogloea ramigera [12], Rhodococcus ruber [13], and Methylobacterium rhodesianum [14]. In R. eutropha the 3-ketothiolase occurs in two different forms, called A and B, which have different substrate specificities [11,15]. In the thiolytic reaction, enzyme A is only active with C4 and C5 3-ketoacyl-CoA whereas the substrate spectrum of enzyme B is much broader, since it is active with C4 to C10 substrates [11]. Enzyme A seems to be the main biosynthetic enzyme acting in the poly(3HB) synthesis pathway, while enzyme B should rather have a catabolic function in fatty-acid metabolism. However, in vitro studies with reconstituted purified enzyme systems have demonstrated that enzyme B can also contribute to poly(3HB) synthesis [15]. 

Unlike catecholamines and indoleamines, histamine itself is not a direct inhibitor of its biosynthetic enzyme, but it exerts feedback control through the H3 autoreceptor. Perhaps the most powerful tool in the study of the histamine system is S-a-fluoromethylhistidine, a highly selective and potent suicide inhibitor of HDC [22]. This compound has been used successfully to study many of the functions of histamine in brain. 

The second area worthy of comment is with regard to assignment of enzyme function based on amino acid sequence alone. In some cases sequence comparisons can be used to determine if a new cDNA encodes one of the well-known flavonoid biosynthetic enzymes. However, in some cases, sequence similarity is insufficient for reliable prediction of the encoded function. For example, the OMTs may have amino acid identities of above 85% but different activities. For transcription factors such sequence-based assignments of function are significantly more difficult, as specific roles for a given factor may have arisen in particular species. Thus, analysis of genetic mutants and transgenic overexpression or knockout lines is still preferable for confirmation of the encoded activities. 

The iron-sulfur proteins include small proteins that function as remarkably simple electron carriers and large multisubunit complexes with multiple activities. Although many of these enzymes function in electron transfer in bioener-getic or biosynthetic pathways, it has become clear that iron-sulfur proteins catalyze a broad array of reactions not always involving electron transfer. 

Type II PKSs such as the bacterial aromatic PKSs are comprised of several mono-or di-domain proteins. Although little is known about the interactions among these proteins, and the relevance of these interactions to enzyme function and selectivity, such interactions are presumably important, given the extremely high lability of the inferred biosynthetic intermediates in these pathways. More recently, protein chemical studies and kinetic analysis have provided evidence for interactions between the ACP and the rest of the minimal PKS, as well as between the auxiliary subunits and the minimal PKS [23,24],... 

Figure 12.18. Output of Pfam search results. Pfam search is performed with amino acid sequence derived from lipoamide dehydrogenase (Schizosaccharomyces pombe). The table for the trusted matches from Pfam-A for pyr redox (pyridine nucleotide disulfide oxidoreductase) and pyr redox dim (pyridine nucleotide disulfide oxidoreductase, dimerization) domains and their alignments (partial) to HMMs ( ->) are shown. The trusted matches from Pfam-B, the potential matches (Thi4 for thiamine biosynthetic enzyme domain), and the bead-on-a-string sketches are not shown. Select the linked domain name to view the functional description of the domain. The HMM alignments are followed by an option button (Align to seed or Align to family) that enables the user to view/save the multiple alignment of each matched family.

Brownfield MS, Yracheta J, Chu F, Lorenz D, Diaz A. Functional chemical neuroanatomy of serotonergic neurons and their targets antibody production and immunohistochemistry (IHC) for 5-HT, its precursor (5-HTP) and metabolite (5-HIAA) biosynthetic enzyme (TPH), transporter (SERT) and three receptors (5-HT2A, 5-HT5A, 5-HT7). Ann NY Acad Sci 1998 861 232-233. 

Porphyria, the disease from which Britain s King George III is believed to have suffered, arises through the accumulation of porphyrin decomposition products in the skin due to impaired enzyme function in the haem biosynthetic pathway [5], In addition to many other unpleasant side effects, porphyria renders the individual highly sensitive to light. The effects of porphyria, if they could be controlled and directed towards particular diseased tissue, would have the potential as a powerful therapeutic method. As the mechanism involves local, light-initiated generation of... 

While the CHS-CHI-F3H-DFR-AS enzymes form the core flavonoid biosynthetic pathway (Fig. 3.2), every intermediate compound in the pathway can be the subject of complex modifications that include hydroxylations, methylations, esterifications, and decorations with a number of sugar moieties. In addition, many of the core enzymes can utilize various substrates resulting in a pathway that is not linear, but rather a complex grid (Fig. 3.2).2 The diverse forms of flavonoids or anthocyanins that accumulate in any plant under any given condition are the result of a combination of the biosynthetic enzymes being expressed together with their substrate specificity. Over the past few years, the structures of several flavonoid biosynthetic enzymes have been elucidated,1 -20 which opens up unlimited opportunities to understand structure-function relationships and to manipulate the pathway. 

The specificity of blends of compounds used for pheromone communication by Lepidoptera species is the result of essentially two distinct sets of biosynthetic enzymes which regulate the production of specific olefinic bonds and synthesis of the oxygenated functional moiety, respectively. In Heliothis moths the regulatory systems that are responsible for production of the functional group during the final stages of pheromone biosynthesis consist of cellular acetate esterases and extracellular alcohol oxidases. Evidence indicates that the relative activities of these enzymes differ for each species of Heliothis. Thus, pheromone mediated reproductive isolation between closely related species of Heliothis is probably the result, in large measure, of the fact that some species require only aldehydes for communication while others use acetates, alcohols and aldehydes. 

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