Reaction specificity in pyridoxal phosphate enzymes

Toney, Michael D.

doi:10.1016/j.abb.2004.09.037

Cited by 260 publications

(248 citation statements)

References 33 publications

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“…5C). By rotating only the dihedral angle of the bound D-serine molecule, we could align the C␣-H bond perpendicular to the coenzyme planar -bonding system, consistent with ␣-proton elimination according to the Dunathan's hypothesis (27,29). Then, the dihedral angle of the D-serine was rotated to allow its hydroxyl group to interact with the zinc ion.…”

Section: Resultsmentioning

confidence: 99%

“…Reaction Specificity-A ␤-hydroxy-␣-amino acid-PLP Schiff base, such as a serine-PLP Schiff base, is theoretically prone to five possible reactions: ␣,␤-elimination, transamination, retroaldol cleavage, decarboxylation, and racemization (29). To examine the reaction specificity of chDSD for D-serine, the products of the chDSD reaction were analyzed.…”

Section: Resultsmentioning

confidence: 99%

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Crystal Structure of a Zinc-dependent d-Serine Dehydratase from Chicken Kidney

Tanaka

Senda

Venugopalan

et al. 2011

Journal of Biological Chemistry

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D-Serine is a co-agonist of the NMDA receptor, an excitatory neurotransmitter receptor important for higher brain functions, including learning and memory (1, 2). The NMDA receptor is a glutamate-gated ion channel (3), and glutamate does not activate the receptor unless a co-agonist binding site is simultaneously occupied by D-serine or glycine (4). Because significant concentrations of D-serine exist in vertebrate brains (5), D-serine is believed to physiologically control the sensitivity of the NMDA receptor to glutamate (6).In mammals, D-serine is produced by a bifunctional serine racemase/dehydratase (7) and is mainly degraded by D-amino acid oxidase (2, 7). In rat brains, the localization of D-amino acid oxidase activity is reciprocal to that of D-serine (8, 9), suggesting that D-amino acid oxidase determines the basal levels of D-serine in mammalian brains. However, we have found recently that, in the chicken brain, D-serine is degraded mainly by a D-serine dehydratase (DSD) 4 (10), which catalyzes the ␣,␤-elimination of water from D-serine to form pyruvate and ammonia. In addition, we have found that the chicken DSD (chDSD) has a primary structure similar to those of metal-activated D-threonine aldolases (11-13), which are fold-type III PLP-dependent enzymes (14), and is distinct from a well known metal-independent bacterial DSD (dsdA) belonging to the foldtype II PLP-dependent enzyme family (14,15). Interestingly, a fold-type III family protein coded by gene YGL196W of Saccharomyces cerevisiae was recently identified as a zinc-dependent DSD (scDSD) (16). To understand why avian species use DSD to metabolize D-serine in the brain and its physiological functions, it is important to reveal the structural and enzymatic properties of this novel DSD family.In the present study, we showed that chDSD requires Zn 2ϩ just as scDSD does. Then, to reveal the catalytic roles of Zn 2ϩ in the dehydration of D-serine, we determined the crystal structures of chDSD, EDTA-treated chDSD, and the EDTA-treated chDSD⅐D-serine complex. Although there is only one DSD entry in the Protein Data Bank (PDB), DSD from Burkholderia xenovorans LB400 (PDB code 3GWQ), the structure contains neither PLP nor zinc, and the enzymatic properties of this DSD *

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Crystal Structure of a Zinc-dependent d-Serine Dehydratase from Chicken Kidney

Tanaka

Senda

Venugopalan

et al. 2011

Journal of Biological Chemistry

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“…To determine the production of GABA, about 2.0 g of each yeast species, where the cell contents of the yeast were adjusted to 2:00 AE 0:01 by measuring the absorbance at 660 nm of yeast cell culture after diluting it 100 times with sterile distilled water, was added to 200-ml conical flasks containing 25 ml each of the following reaction solutions: (A) a solution containing 1% monosodium glutamate, (B) a solution containing 5% glucose, and (C) a solution containing 1% monosodium glutamate and 5% glucose. The pH of the reaction solutions was adjusted to 6.0 with 2 N HCl or 2 N NaOH solution and incubated at 37 C for 72 h on a rotary shaker at 120 rpm. The reaction solutions were then heated at 85 C for 15 min and subjected to centrifugation at 6;000 Â g for 15 min.…”

Section: Methodsmentioning

confidence: 99%

Isolation of Marine Yeasts Collected from the Pacific Ocean Showing a High Production of γ-Aminobutyric Acid

Masuda¹,

Guo²,

Uryu³

et al. 2008

Bioscience, Biotechnology, and Biochemistry

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Marine yeasts were collected from coastal and deep sea areas in the Pacific Ocean and the Sea of Japan around central and northern Japan to prepare a novel type of natural seasoning. It was found that one of the marine yeasts collected from the Pacific Ocean off Hachinohe showed a high concentration of -aminobutyric acid (GABA) in its extract, about 7-10 times higher than those of commercially available bread yeast and other marine yeasts. The marine yeast isolated and named Hachinohe No. 6 catalyzed the reaction from monosodium glutamate to GABA only in the presence of glucose. Subsequently, several marine yeasts belonging to the genera Pichia and Candida were found to have such catalytic activities, but not those belonging to the genus Saccharomyces. Isolate Hachinohe No. 6 was found to have the highest catalytic activity among the yeasts examined in this study.

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“…Crenarchaea that grow at even higher temperatures, such as Pyrobaculum aerophilum (100°C growth optimum), appear to have no PLP-dependent decarboxylases (they use an ␣-aminoadipate pathway for lysine biosynthesis instead of a diaminopimelate pathway). At high temperatures, the selectivity of these enzymes for decarboxylation may decrease, leading to inactivating side reactions (40). Further studies on the temperature dependence of these side reactions are needed to compare the pyruvoyl and PLP-dependent decarboxylases.…”

Section: Discussionmentioning

confidence: 99%

Crenarchaeal Arginine Decarboxylase Evolved from an S-Adenosylmethionine Decarboxylase Enzyme

Giles

Graham

2008

Journal of Biological Chemistry

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The crenarchaeon Sulfolobus solfataricus uses arginine to produce putrescine for polyamine biosynthesis. However, genome sequences from S. solfataricus and most crenarchaea have no known homologs of the previously characterized pyridoxal 5-phosphate or pyruvoyl-dependent arginine decarboxylases that catalyze the first step in this pathway. Instead they have two paralogs of the S-adenosylmethionine decarboxylase (AdoMetDC). The gene at locus SSO0585 produces an AdoMetDC enzyme, whereas the gene at locus SSO0536 produces a novel arginine decarboxylase (ArgDC). Both thermostable enzymes self-cleave at conserved serine residues to form amino-terminal ␤-domains and carboxyl-terminal ␣-domains with reactive pyruvoyl cofactors. The ArgDC enzyme specifically catalyzed arginine decarboxylation more efficiently than previously studied pyruvoyl enzymes. ␣-Difluoromethylarginine significantly reduced the ArgDC activity of purified enzyme, and treating growing S. solfataricus cells with this inhibitor reduced the cells' ratio of spermidine to norspermine by decreasing the putrescine pool. The crenarchaeal ArgDC had no AdoMetDC activity, whereas its AdoMetDC paralog had no ArgDC activity. A chimeric protein containing the ␤-subunit of SSO0536 and the ␣-subunit of SSO0585 had ArgDC activity, implicating residues responsible for substrate specificity in the amino-terminal domain. This crenarchaeal ArgDC is the first example of alternative substrate specificity in the AdoMetDC family. ArgDC activity has evolved through convergent evolution at least five times, demonstrating the utility of this enzyme and the plasticity of amino acid decarboxylases.The Crenarchaeota include the most hyperthermophilic cultivated microorganisms. To help stabilize macromolecules in these extreme conditions, some hyperthermophiles produce unusually long chain or branched polyamines (1).Chromatographic analyses of extracts from the crenarchaeon Sulfolobus solfataricus identified significant amounts of the linear polyamines 1,3-diaminopropane, putrescine, sym-norspermidine (caldine), spermidine, and sym-norspermine (thermine), with traces of spermine (2, 3). The biosynthesis of the spermidine and spermine polyamines was predicted to follow a canonical eukaryotic pathway, where the decarboxylation of L-ornithine produces putrescine, and S-adenosyl-L-methionine (AdoMet) 2 is decarboxylated to form the propylamine donor S-(5Ј-adenosyl)-3-methylthiopropylamine (dcAdoMet) (4). Subsequently, the AdoMet decarboxylase (AdoMetDC) (5) and propylamine transferase (6) enzymes were purified from S. solfataricus. The latter enzyme produces spermidine and spermine from putrescine and dcAdoMet, and it produces norspermidine and norspermine from 1,3-diaminopropane and dcAdoMet (Fig.

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Reaction specificity in pyridoxal phosphate enzymes

Cited by 260 publications

References 33 publications

Crystal Structure of a Zinc-dependent d-Serine Dehydratase from Chicken Kidney

Crystal Structure of a Zinc-dependent d-Serine Dehydratase from Chicken Kidney

Isolation of Marine Yeasts Collected from the Pacific Ocean Showing a High Production of γ-Aminobutyric Acid

Crenarchaeal Arginine Decarboxylase Evolved from an S-Adenosylmethionine Decarboxylase Enzyme

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