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At least 1,063 records · Page 59Linked to original sources
PubMed1996

Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.

D-amino acid oxidase is the prototype of the FAD-dependent oxidases. It catalyses the oxidation of D-amino acids to the corresponding alpha-ketoacids. The reducing equivalents are transferred to molecular oxygen with production of hydrogen peroxide. We have solved the crystal structure of the complex of D-amino acid oxidase with benzoate, a competitive inhibitor of the substrate, by single isomorphous replacement and eightfold averaging. Each monomer is formed by two domains with an overall topology similar to that of p-hydroxybenzoate hydroxylase. The benzoate molecule lays parallel to the flavin ring and is held in position by a salt bridge with Arg-283. Analysis of the active site shows that no side chains are properly positioned to act as the postulated base required for the catalytic carboanion mechanism. On the contrary, the benzoate binding mode suggests a direct transfer of the substrate alpha-hydrogen to the flavin during the enzyme reductive half-reaction. The active site Of D-amino acid oxidase exhibits a striking similarity with that of flavocytochrome b2, a structurally unrelated FMN-dependent flavoenzyme. The active site groups (if these two enzymes are in fact superimposable once the mirror-image of the flavocytochrome b2 active site is generated with respect to the flavin plane. Therefore, the catalytic sites of D-amino acid oxidase and flavocytochrome b2 appear to have converged to a highly similar but enantiomeric architecture in order to catalvze similar reactions (oxidation of alpha-amino acids or alpha-hydroxy acids), although with opposite stereochemistry.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMed2003

Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae.

A bright, saffron-colored marine bacterium HTCC2559T was isolated from the Bermuda Atlantic Time Series station in the western Sargasso Sea, Atlantic Ocean by high throughput culturing methods and characterized by polyphasic approaches. Phenotypic data and phylogenetic analyses showed that the strain is a member of the family Flavobacteriaceae. The strain was gram-negative, non-motile, chemoheterotrophic, strictly aerobic, NaCl-requiring, rod-shaped cells that contain carotenoid pigments but not flexirubin. Several kinds of macromolecules (gelatin, DNA, starch, casein, and elastin) were degraded and carbohydrates, sugar alcohols, organic acids, and amino acids were utilized as sole carbon sources. The dominant fatty acids were branched or hydroxy acids, and 3-OH i17:0, i15:0, i15:1, and i17:1 omega9c were abundant. The DNA G+C content of the strain is 34.8 mol%. Phylogenetic analyses using three treeing algorithms based on 16S rRNA gene sequences revealed that the strain formed a very distinct lineage that is allied closely with several seawater environmental clones in the family Flavobacteriaceae. Therefore, it is proposed from the polyphasic studies that strain HTCC2559T (=ATCC BAA-628T = KCTC 12090T) belongs to a new genus and species named Croceibacter atlanticus gen. nov., sp. nov.

Biodegradation, Environmental↗
PubMed2004

C18 hydroxy fatty acids as markers of lipid peroxidation ex vivo and in vivo.

Different C18 monohydroxy fatty acids (OHFAs) were evaluated for their usefulness as markers of plasma lipid peroxidation (unsaturated fatty acid oxidation) ex vivo and in vivo. First, plasma samples (n = 5) were exposed for 3 h to different radical fluxes ex vivo. The formation of OHFAs was assessed by using varying concentrations of Cu2+ ions and AAPH (2,2'-azobis(2-amidinopropane) hydrochloride) as radical flux initiators. Secondly, a cross-sectional study was carried out in 47 middle-aged men. In this study, plasma concentrations of different in vivo OHFAs were compared with other indices of lipid peroxidation. Under mild oxidation conditions (heparin plasma containing 4.2 or 8.3 mM AAPH), concentrations of all the measured OHFAs (8, 9, 10, 11, 12, 13, 15 and 16-OH acids) increased in an identical manner, but under highly oxidative conditions (heparin plasma containing 83 mM AAPH or 4.2 to 8.3 mM CuSO4) mainly 9 and 13-OHFAs were formed. In the cross-sectional study, plasma 11 and 13-OHFA levels were associated statistically significantly with plasma free F2alpha-isoprostanes, recognized index of in vivo lipid peroxidation (r = 0.305, p = 0.037 and r = 0.308, p = 0.035, respectively). In addition, 16-OHFA levels correlated with the ratio of electronegatively charged LDL to total LDL (r = 0.335, p = 0.021). With respect to the other OHFAs, 15-OHFA had no correlation with either other OHFAs or the reference substances used. In addition, occasionally there were contamination problems in the assessment of 12-OHFA. It is concluded that all of the measured C18 OHFAs can be used as indicators of plasma lipid peroxidation under mild oxidation conditions, though the 12 and 15-OHFAs may need to be used with some caution. Under high oxidation conditions, 9-and 13-OHFAs seem to be the most useful indices because of their high formation capacity.

Antioxidants↗
PubMed1979

Generation of unique mono-hydroxy-eicosatetraenoic acids from arachidonic acid by human neutrophils.

Incubation of [3H]arachidonic acid with the 17,000-g supernatant from homogenates of human neutrophils in the presence of indomethacin generated the unique metabolites 9-OH-5,7,11,14-eicosatetraenoic acid (9-HETE) and 8-HETE, in addition to 12-HETE, 11-HETE and 5-HETE. The human neutrophil chemotactic activity of the HETE products exhibited a rank-order of potency with 5-HETE greater than 8-HETE = 9-HETE greater than 11-HETE = 12-HETE. The expression of chemokinetic activity as well as chemotactic activity suggested that the endogenous production of these principles may influence the mobility of human neutrophils.

Arachidonic Acids↗
PubMed1993

Chemical peeling.

This article explores the wide range of chemical facial peels, which include phenol, trichloroacetic acid, and alpha-hydroxy acids. The application of these substances will be described in addition to the contraindications to this type of treatment.

Chemexfoliation↗
PubMed1997

Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids.

Strains of Meiothermus cerbereus sp. nov. were isolated from the hot springs within the Geysir geothermal area of Iceland. The strains of Meiothermus cerbereus produce red-orange-pigmented colonies, have an optimum growth temperature of about 55 degrees C, and have higher levels of 3-OH fatty acids than the strains of the other species of the genus Meiothermus. These strains, unlike all other strains of the species of the genus Meiothermus examined previously, required cysteine, thiosulfate, or thioglycolate for growth in liquid Thermus medium, but not in the corresponding medium solidified with agar. Several strains belonging to Meiothermus silvanus, isolated from Geysir, also required reduced sulfur compounds for growth in liquid medium, leading to the hypothesis that this requirement is not a taxonomic characteristic of the new species. The new species represented by strains GY-1T and GY-5 can be distinguished from the other species of the genus Meiothermus by biochemical characteristics, fatty acid composition, DNA-DNA reassociation values, and 16S ribosomal DNA sequence. The type strain for Meiothermus cerbereus is GY-1 (= DSM 11376).

Base Composition↗
PubMed2004

Robiginitalea biformata gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae with a higher G+C content.

Two Gram-negative, chemoheterotrophic, non-motile, rust-coloured, marine strains were isolated from the western Sargasso Sea by high-throughput culturing. Characterization of the two strains by polyphasic approaches indicated that they are members of the same species. Phylogenetic analyses based on 16S rRNA gene sequences using three treeing algorithms revealed that the strains formed a coherent and novel genus-level lineage within the family Flavobacteriaceae. The dominant fatty acids were branched or hydroxy acids, i15 : 0, i15 : 1 and 3-OH i17 : 0 being the most abundant. The higher DNA G+C content of the strains (55-56 mol%) clearly differentiated them from other genera of the family Flavobacteriaceae (27-44 mol%). It is proposed, from the polyphasic evidence, that the strains be placed into a novel genus and a novel species named Robiginitalea biformata gen. nov., sp. nov., with strain HTCC2501T (=ATCC BAA-864T=KCTC 12146T) as the type strain.

Atlantic Ocean↗
PubMed2006

Krokinobacter gen. nov., with three novel species, in the family Flavobacteriaceae.

Five strains belonging to the family Flavobacteriaceae were isolated from marine-sediment samples collected in Sagami and Tokyo bays on the Pacific coastline of Japan. The five isolates formed a coherent and novel genus-level lineage within the family Flavobacteriaceae. The most closely related species with a validly published name was Cellulophaga lytica. The five isolates were rod-shaped, Gram-negative, aerobic, catalase- and oxidase-positive, flexirubin-negative and yellow-pigmented. The dominant fatty acids were branched or hydroxy acids, i.e. i-C(15:0), i-C(15:1) and i-C(17:0) 3-OH. These strains degraded gelatin, casein, DNA and Tween 80. The G+C content of their DNAs ranged between 33 and 39 mol%. Although analysis of the 16S rRNA gene sequence similarity divided these strains into two subgroups with a 2.3% sequence difference, the results of DNA-DNA hybridization indicated the grouping of these strains into three distinct species. On the basis of phenotypic and genotypic analyses, the novel genus Krokinobacter is proposed, with Krokinobacter genikus sp. nov., containing three of the strains, as the type species. The type strain is Cos-13T (=NBRC 100811T=CIP 108744T). The names Krokinobacter eikastus sp. nov. (type strain PMA-26T=NBRC 100814T=CIP 108743T) and Krokinobacter diaphorus sp. nov. (type strain MSKK-32T=NBRC 100817T=CIP 108745T) are proposed for the other two isolates.

Bacterial Typing Techniques↗
PubMed1989

Covalently bound lipids of human stratum corneum.

In the present study, we demonstrate that human stratum corneum contains covalently bound lipids accounting for 1.4% of the dry weight of the tissue. The major component (53.3% of the total by weight) is a ceramide (CER-A) consisting of 30 through 34-carbon omega-hydroxyacids amide-linked to sphingosine. The other bound lipids in human stratum corneum include fatty acids (12.7%), omega-hydroxy acids (9.4%), and a second, more polar, omega-hydroxyacid-containing ceramide (CER-B, 24.8%). The predominant omega-hydroxyacids in both ceramides, as well as the free hydroxyacid fraction, are the 30-carbon saturated and 32- and 34-carbon monoenoic species. The bound fatty acids consist largely of 14 through 22-carbon saturated species, but significant proportions of monoenoic species and linoleic acid are also present. Psoriatic scale contains a similar total concentration of the same covalently bound lipids, but the proportions of the individual bound lipids are different from those found in normal stratum corneum. It is suggested that the principal function of the covalently bound lipids in human stratum corneum is the formation of a lipid envelope on the outer surface of the keratinized cells.

Animals↗