Structural study on a naturally occurring terphenyl quinone.

Two terphenyl quinones were synthesized for a structural study on a naturally occurring biologically active terphenyl quinone. 3-Methoxy-5,6-diphenylcyclohexa-3,5-dien-1,2-dione, a possible structure proposed by our analysis of the NMR spectra, was synthesized by Suzuki-Miyaura coupling and subsequent oxidation of the resulting substituted phenol, although not being identical to the natural product. Recently isolated 3-methoxy-2,5-diphenylcyclohexa-2,5-dien-1,4-dione was synthesized from a commercially available 2,5-diphenyl-1,4-benzoquinone in three steps in a good overall yield, and its NMR spectra were identical to those of the natural product.

Structure of two purple pigments, catechiopyranocyanidins A and B from the seed-coat of the small red bean, Vigna angularis.

The small red bean, Vigna angularis, is primarily used to produce the "an-paste" component of Japanese sweets. Through the manufacturing process, the red seed-coat pigment is transferred to the colorless "an-particles", imparting a purple color. However, the major pigment in the seed coat has not yet been identified, although it is historically presumed to be an anthocyanin. Here, we report the isolation and structural determination of two hydrophobic purple pigments in the seed coat via instrumental analysis and derivatization. The new pigments, catechinopyranocyanidins A and B, contain a novel pyranoanthocyanidin skeleton condensed with a catechin and cyanidin ring system, and no sugar moieties. Catechinopyranocyanidins A and B are diastereomers with a different configuration at the catechin moiety, and both are purple in color in strongly acidic-to-neutral media. Catechinopyranocyanidins A and B are very stable under dark conditions, but, labile to light and decompose to colorless compounds. Thus, these pigments exhibit quite different chemical properties compared to simple anthocyanidins.

Author Correction: Structure of two purple pigments, catechinopyranocyanidins A and B from the seed-coat of the small red bean, Vigna angularis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Streptomyces phospholipase D mutants with altered substrate specificity capable of phosphatidylinositol synthesis.

The substrate specificity of a phospholipase D (PLD) from Streptomyces antibioticus was altered by site-directed saturation mutagenesis, so that it was able to synthesize phosphatidylinositol (PI). Mutations were introduced in the pld gene at the positions corresponding to three amino acid residues that might be involved in substrate recognition, and the mutated genes were expressed in Escherichia coli BL21 (DE3). High-throughput screening of approximately 10,000 colonies for PI-synthesizing activity identified 25 PI-synthesizing mutant PLDs. One of these mutant enzymes was chosen for further analysis. The structure of the PI synthesized with the mutant enzyme was analyzed by HPLC-MS and NMR. It was found that the mutant enzyme generated a mixture of structural isomers of PIs with the phosphatidyl groups connected at different positions of the inositol ring. The phosphatidylcholine-hydrolyzing activity of the mutant PLD was much lower than that of the wild-type enzyme. The mutant enzyme was able to transphosphatidylate various cyclohexanols with a preference for bulkier compounds. This is the first example of alteration of the substrate specificity of PLD and of PI synthesis by Streptomyces PLD.

A cis-prenyltransferase from Methanosarcina acetivorans catalyzes both head-to-tail and nonhead-to-tail prenyl condensation.

Cis-prenyltransferase usually consecutively catalyzes the head-to-tail condensation reactions of isopentenyl diphosphate to allylic prenyl diphosphate in the production of (E,Z-mixed) polyprenyl diphosphate, which is the precursor of glycosyl carrier lipids. Some recently discovered homologs of the enzyme, however, catalyze the nonhead-to-tail condensation reactions between allylic prenyl diphosphates. In this study, we characterize a cis-prenyltransferase homolog from a methanogenic archaeon, Methanosarcina acetivorans, to obtain information on the biosynthesis of the glycosyl carrier lipids within it. This enzyme catalyzes both head-to-tail and nonhead-to-tail condensation reactions. The kinetic analysis shows that the main reaction of the enzyme is consecutive head-to-tail prenyl condensation reactions yielding polyprenyl diphosphates, while the chain lengths of the major products seem shorter than expected for the precursor of glycosyl carrier lipids. On the other hand, a subsidiary reaction of the enzyme, i.e., nonhead-to-tail condensation between dimethylallyl diphosphate and farnesyl diphosphate, gives a novel diterpenoid compound, geranyllavandulyl diphosphate.

Reaction mechanism of Zn2+-dependent d-serine dehydratase: role of a conserved tyrosine residue interacting with pyridine ring nitrogen of pyridoxal 5'-phosphate.

d-Serine dehydratase from Saccharomyces cerevisiae (Dsd1p) is a pyridoxal 5'-phosphate (PLP)- and Zn(2+)-dependent enzyme that catalyzes the dehydration of d-serine to yield pyruvate and ammonia. Dsd1p uses the Tyr residue (Y203) to interact with the pyridine nitrogen of PLP, which is a unique feature of PLP enzymes. To investigate the role of Y203 in catalysis, a series of Y203 mutants was constructed and studied. Mutant enzymes possessing a non-polar or a basic residue instead of Y203 (Y203F, A, S and R) exhibited substantial levels of catalytic activity, and among these, the Y203F mutant had the least impact on catalytic activity. The Y203D exhibited a 10(5)-fold decrease in enzyme activity, and unlike wild-type enzyme, the mutant enzyme favoured the Cα reprotonation before hydroxyl group protonation. Our data show that the Y203 does not participate in the protonation of the pyridine nitrogen (N1) of PLP, and Dsd1p uses the cofactor in an N1-unprotonated state. The unprotonated N1 promotes elimination of the leaving group and evades Cα reprotonation before hydroxyl group protonation.

Role of zinc ion for catalytic activity in d-serine dehydratase from Saccharomyces cerevisiae.

d-Serine dehydratase from Saccharomyces cerevisiae (DsdSC) is a fold-type III pyridoxal 5'-phosphate-dependent enzyme catalyzing d-serine dehydration. The enzyme contains 1 mol Zn(2+) in its active site and shows a unique zinc dependence. The Zn(2+) is essential for the d-serine dehydration, but not for the α,ß-elimination of ß-Cl-d-alanine catalyzed as a side-reaction. The fact that dehydration of d-threonine and d-allo-threonine, also catalyzed by DsdSC, is likewise Zn(2+) dependent indicates that Zn(2+) is indispensable for the elimination of hydroxyl group, regardless of the stereochemistry of C(ß) . Removal of Zn(2+) results in a less polar active site without changing the gross conformation of DsdSC. (1) H NMR determined the rates of α-hydrogen abstraction and hydroxyl group elimination of d-serine in (2) H(2) O to be 9.7 and 8.5 s(-1) , respectively, while the removal of Zn(2+) abolished both reactions. Mutation of Cys400 or His398 within the Zn(2+) binding sites to Ala endowed DsdSC with similar properties to those of the Zn(2+) -depleted wild-type enzyme: the mutants lost the reactivity toward d-serine and d-threonine but retained that toward ß-Cl-d-alanine. (1) H NMR analysis also revealed that both α-hydrogen abstraction and hydroxyl group elimination from d-serine were severely hampered in the C400A mutant. Our data suggest that DsdSC catalyzes the α-hydrogen abstraction and hydroxyl group elimination in a concerted fashion.

Malyngamide X: the first (7R)-lyngbic acid that connects to a new tripeptide backbone from the Thai sea hare Bursatella leachii.

Malyngamide X (1), the first (7R)-lyngbic acid connected to a new tripeptide backbone, was isolated from the Thai sea hare Bursatella leachii. The gross structure of 1 was established on the basis of 1D and 2D NMR and mass spectroscopic data. Combination of the NMR spectroscopic experiments with alpha-methoxy-alpha-(trifluoromethyl)phenylacetic acid esters, 2,2,2-trifluoro-1-(9-anthryl)ethanol chiral solvating agent, and molecular mechanics of 1 and the synthetic molecular fragments allowed us to determine the absolute stereochemistry of all six stereogenic centers without hydrolytic degradation of the compound. Compound 1 displayed moderate cytotoxic, antitubercular, and antimalarial properties.

Tetrabromohydroquinone and riboflavin are possibly responsible for green luminescence in the luminous acorn worm, Ptychodera flava.

2,3,5,6-Tetrabromohydroquinone was isolated as a luminous substance from Ptychodera flava. This compound emitted light after addition of hydrogen peroxide under basic conditions. Since hydroquinone had no fluorescence, further investigation by spectral analysis revealed that riboflavin was the only possible light emitter having green fluorescence. In the presence of both tetrabromohydroquinone and riboflavin under a basic condition containing 70% 1,4-dioxane, green light emission was observed following the addition of hydrogen peroxide. We succeeded in recording the same emission spectrum as that in the bioluminescence caused by the addition of aqueous diluted hydrogen peroxide solution in P. flava.

Complexation of cyclic dodecadepsipeptide, cereulide with ammonium salts.

Cereulide is a principal toxin causing emetic syndrome which is produced by Bacillus cereus and has been known as potassium selective ionophore. This paper deals with its complexation with inorganic and organic ammonium ions to assign the higher structures similar to the complex with potassium ion by means of NMR and ESI-MS spectroscopy. Of particular interest, the detectable ions are not only at m/z 1191.8 as K(+) complex but also (or sometimes exclusively) at m/z 1170.8 as NH(4)(+) complex in its LC-MS analyses depending upon the conditions. This difference is due to the sample preparation and measurement condition.