2-Deoxyribose-5-phosphate aldolase of Salmonella typhimurium: Purification and properties

Hoffee, Patricia A.

doi:10.1016/0003-9861(68)90473-6

Cited by 61 publications

(28 citation statements)

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“…They do, however, share the common phosphatebinding site located between β7 and β8 [15,20]. Furthermore, the fact that the family of deoxyribose 5-phosphate aldolases (DeoC) shows similarity to both classes of FBPAs, and thus might represent an intermediate form between FBPA I and II, supports the notion of common ancestry [11,21].…”

Section: The Classical and Archaeal Fbpas I Are Homologousmentioning

confidence: 84%

Structure, function and evolution of the Archaeal class I fructose-1,6-bisphosphate aldolase

Lorentzen

Siebers

Hensel

et al. 2004

Biochemical Society Transactions

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FBPA (fructose-1,6-bisphosphate aldolase) catalyses the reversible aldol condensation of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate to form fructose 1,6-bisphosphate. Two classes of FBPA, which rely on different reaction mechanisms, have so far been discovered, class I mainly found in Eucarya and class II mainly in Bacteria. Only recently were genes encoding proteins with FBPA activity identified in Archaea. Archaeal FBPAs do not share any significant overall sequence identity with members of the traditional classes of FBPAs, raising the interesting question of whether they have evolved independently by convergent evolution or diverged from a common ancestor. Biochemical characterization of FBPAs of the two hyperthermophilic Archaea Thermoproteus tenax and Pyrococcus furiosus showed that the enzymes use a Schiff-base mechanism and thus belong to the class I aldolases. The crystal structure of the archaeal FBPA from T. tenax revealed that the protein fold, as for the classical FBPA I and II, is that of a parallel (betaalpha)(8) barrel. A substrate-bound crystal structure allowed detailed active-site comparisons which showed the conservation of six important catalytic and substrate-binding residues between the archaeal and the classical FBPA I. This observation provides further evidence that the two sequence families of proteins share a common evolutionary origin. Furthermore, structure and sequence analysis indicate that the class I FBPA shares a common evolutionary origin with several other enzyme superfamilies of the (betaalpha)(8) barrel fold.

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Section: The Classical and Archaeal Fbpas I Are Homologousmentioning

confidence: 84%

Structure, function and evolution of the Archaeal class I fructose-1,6-bisphosphate aldolase

Lorentzen

Siebers

Hensel

et al. 2004

Biochemical Society Transactions

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“…typhimurium (Hoffee, 1968a), the activity of the enzyme in Group N streptococci was not stimulated by citrate.…”

Section: Resultsmentioning

confidence: 82%

“…Deoxyriboaldolase can be induced in Escherichia coli by thymidine (MunchPetersen, 1968a) andin L. plantarum 8041 (Pricer &Horecker, 1960) and Salmonella typhimurium (Hoffee, 19686) by 2-deoxyribose. L. plantarum 8041 contained deoxyriboaldolase only when grown in the presence of 2-deoxyribose ( Table 3) in confirmation of the results of Pricer & Horecker (1960).…”

Section: Resultsmentioning

confidence: 99%

“…3) and deoxyribomutase (Table 2) activities in strain DRC3, although low, showed that this organism may degrade thymidine to acetaldehyde and glyceraldehyde-3-phosphate (Table 2) using a similar pathway to that found in Sal. typhimurium (Hoffee, 19686;Hoffee & Robertson, 1969) and in E. coli (Lomax & Greenberg, 1968;Munch-Petersen, 1968a, 6). Acetaldehyde was the only volatile compound detected when thymidine, 2-deoxyribose-1-phosphate and 2-deoxyribose-5-phosphate were incubated with cellfree extracts of strain DRC3.…”

Section: Resultsmentioning

confidence: 99%

“…This enzyme is thought to be involved in the degradation rather than the synthesis of DNA (Sable, 1966). Thymidine which is formed by the breakdown of DNA is degraded by the enzymes thymidine phosphorylase and deoxyribomutase to 2-deoxyribose-5-phosphate (Hoffee, 19686; Hoffee & Robertson, 1969;Hoffmann & Lampen, 1952; Munch-Petersen, 1968 a, b). Although the presence of deoxyriboaldolase is widespread among bacterial species, its presence and activity are not essential for growth of the organism.…”

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confidence: 99%

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Formation of acetaldehyde from 2-deoxy-D-ribose-5- phosphate in lactic acid bacteria

Lees

Jago

1977

Journal of Dairy Research

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Acetaldehyde can be formed from 2-deoxyribose-5-phosphate by organisms which contain the enzyme deoxyriboaldolase. This enzyme is thought to be involved in the degradation rather than the synthesis of DNA (Sable, 1966). Thymidine which is formed by the breakdown of DNA is degraded by the enzymes thymidine phosphorylase and deoxyribomutase to 2-deoxyribose-5-phosphate (Hoffee, 19686; Hoffee & Robertson, 1969;Hoffmann & Lampen, 1952; Munch-Petersen, 1968 a, b). Although the presence of deoxyriboaldolase is widespread among bacterial species, its presence and activity are not essential for growth of the organism. Mutants of Escherichia coli (Munch-Petersen, 1968a) which lack this enzyme are known.J This paper describes the activity and properties of the deoxyriboaldolase in lactic acid bacteria and the possible breakdown of thymidine to acetaldehyde in these organisms. MATEEIALS AND METHODSThe lactic acid bacteria examined, media, growth conditions, and the preparation of cell-free extracts have been described previously (Lees & Jago, 1976). When required, the pH of the growth medium was maintained at a constant value by the addition of 10 M-NaOH controlled by a magnetic valve (Radiometer, Model MNV1, Copenhagen, Denmark) connected to a titrator (Radiometer, Model TTTllb).Deoxyriboaldolase (E.C. 4.1.2.4) activity, measured in the direction of synthesis of 2-deoxyribose-5-phosphate, was estimated by the method of Racker (1952). The reaction mixture, total volume 2-6 ml, contained: 15/nnoles of fructose-1,6-diphosphate; 52 /imoles of acetaldehyde (or water); 50 fondles of triethanolamine-HCl buffer, pH 6-5; 30 fig aldolase (optional) and 0-25 ml (c. 4 mg protein) of a bacterial cell-free extract. The reaction mixtures were incubated for 30 min at 37 °C before the reaction was stopped by the addition of 0-5 ml]of 20 % (w/v) TCA. Deoxyribose phosphate was estimated in 1 ml samples by the diphenylamine method (Racker, 1952).When deoxyriboaldolase activity was assayed in the direction of breakdown of 2-deoxyribose-5-phosphate (forming acetaldehyde and glyceraldehyde-3-phosphate), the reaction mixture was added to the outer well of a Conway microdiffusion unit and the acetaldehyde formed was absorbed into semicarbazide in the centre well and

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Aldol Reaction – Biological and Biomimetic

Dickerson

Córdova

Chen

et al. 2002

Encyclopedia of Catalysis

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In order to develop new methodology for stereospecific and catalytic aldol reactions, synthetic organic chemists are now exploring the utility of biological catalysts. There has been significant progress in this field and several efficient, selective, and predictable biological catalysts are now available for the asymmetric aldol reaction. Critical to metabolism, the aldolases catalyze in vivo aldol reactions with high chemo‐, regio‐, diastereo‐, and enantioselectivity. These enzymes are divided into four distinct areas: DHAP‐dependent, pyruvate/phosphoenol pyruvate‐dependent, acetaldehyde‐dependent, and glycine‐dependent aldolases based upon their donor dependence. Catalytic antibodies that operate via a mechanism reminiscent of a type I aldolase also have been developed. These antibodies have remarkable rate accelerations and broader substrate specificity compared to naturally occurring aldolases. However, both aldolases and catalytic antibodies share a common feature critical to their success as synthetically useful catalysts—both are capable of tolerating substrates with unprotected functional groups in aqueous solutions and give readily predictable products. This article will focus on the development of these two areas of biological aldol catalysts and discuss relevant examples as appropriate.

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2-Deoxyribose-5-phosphate aldolase of Salmonella typhimurium: Purification and properties

Cited by 61 publications

References 20 publications

Structure, function and evolution of the Archaeal class I fructose-1,6-bisphosphate aldolase

Structure, function and evolution of the Archaeal class I fructose-1,6-bisphosphate aldolase

Formation of acetaldehyde from 2-deoxy-D-ribose-5- phosphate in lactic acid bacteria

Aldol Reaction – Biological and Biomimetic

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