The full-length, protein coding sequence for dehaloperoxidase was obtained using a reverse genetic approach and a cDNA library from marine worm Amphitrite ornata. The crystal structure of the dehaloperoxidase (DHP) was determined by the multiple isomorphous replacement method and was refined at 1.8-Å resolution. The enzyme fold is that of the globin family and, together with the amino acid sequence information, indicates that the enzyme evolved from an ancient oxygen carrier. The peroxidase activity of DHP arose mainly through changes in the positions of the proximal and distal histidines relative to those seen in globins. The structure of a complex of DHP with 4-iodophenol is also reported, and it shows that in contrast to larger heme peroxidases DHP binds organic substrates in the distal cavity. The binding is facilitated by the histidine swinging in and out of the cavity. The modeled position of the oxygen atom bound to the heme suggests that the enzymatic reaction proceeds via direct attack of the oxygen atom on the carbon atom bound to the halogen atom.Polychlorinated phenols and other polychlorinated aromatics of anthropogenic origin have been widely dispersed and constitute significant environmental problems. It is less known that bromoaromatics of biotic origin are also widespread and secreted as chemical warfare by a number of marine organisms. Dehalogenating enzymes are used as the first line of defense against these toxicants by organisms that live in such contaminated environments (1). We have recently discovered and characterized by a number of techniques (2-4) an enzyme with a novel function, dehaloperoxidase (DHP).1 DHP is isolated from Amphitrite ornata, a terebellid polychaete. This species does not produce halogenated compounds itself but usually co-habits estuarine mud flats with other polychaete worms, such as Notomastus lobatus, and hemichordata such as Saccoglossus kowalewskyi, which secrete large quantities of brominated aromatics and other halometabolites as repellents (5). The levels of DHP are very high as it represents approximately 3% of the soluble protein in crude extracts of A. ornata. The enzyme catalyzes the oxidative dehalogenation of polyhalogenated phenols in the presence of hydrogen peroxide at a rate at least 10 times faster than all known halohydrolases of bacterial origin, according to Reaction 1.The oxidative potential of hydrogen peroxide likely allows for the unusually high rate of this reaction as well as for the unique ability of DHP to dehalogenate fluorophenols. The enzyme has activity toward substrates with different numbers and positions of halogen substituents (2).The binding of oxygen and peroxide ligands and their activation are due to the presence of heme in a variety of oxygen carriers and enzymes. This is also true for DHP, which contains one heme per subunit (3) and a histidine as the proximal iron ligand (4). The propensity of peroxidases (and oxygenases, which tend to have a cysteinate proximal ligand) to cleave the oxygen-oxygen bond and form a high vale...
JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. This content downloaded from 128.235.251.160 on Tue, Abstract. Disturbance is a significant mortality source in many assemblages. The susceptibility of organisms to this mortality source is, in part, a function of the availability of substrate heterogeneities that act as refuges from the disturbance process. There are at least 5 major categories of temporal and spatial refuges from disturbance: (1) temporal periods outside the activity range of the disturbance process; (2) temporal periods within the activity range of the disturbance process; (3) spatial zones beyond the activity range of the disturbance process; (4) physical heterogeneities within the activity range of the disturbance process; and (5) biologically generated refuges within the activity range of the disturbance process.The last category is particularly interesting because it involves an organism's utilization of a refuge which is the product of another organism or organisms. Data from a marine system are used to demonstrate the effectiveness of several types of refuges, particularly biologically generated refuges. The refuge-forming species is Diopatra cuprea, an onuphid polychaete which inhabits shallow water, medium-grained sand flats from Cape Cod to Florida. The abundance and species richness of other members of the infauna are shown to be positively associated with the presence of the tubes of Diopatra. This effect is confined to the area immediately surrounding the tubes of Diopatra. I demonstrated experimentally that a tube-like structure, such as a plastic straw, has the same effect on the infauna as does the tube of Diopatra. Thus, as predicted, the physical and biological refuges affect infaunal abundances similarly. They should not show similar patterns of distribution in space and time however and this is discussed.
Samples of infauna and measurements of temperature, oxygen, salinity, and algal cover were taken from January 1969 to December 1970 at —1.2—ft tidal elevation in a mud flat dominated by polychaetes in Mitchell Bay, San Juan Island, Washington. Mortality of adults after spawning and variable larval settlement success probably explained much of the variation in population numbers of the four large and numerically important polychaete species, Lumbrineris inflata, Axiothella rubrocincta, Platynereis bicanaliculata, and Armandia brevis. No correlations were found between the abundances of numerically important species and physical factors. Exclosures constructed of 3—mm mesh plastic screening placed on the flat became covered with diatoms. Settling juveniles of tube—building species, such as P. bicanaliculata, Axiothella rubrocincta, and L. inflata, built tubes in this layer of diatoms and thus did not reach the enclosed sediment, while settling juveniles of a burrowing species, Armandia brevis, burrowed through the diatom layer and reached the sediment. Thus, cleaning the cage surfaces or removing the cage after settlement reduced abundances of tube—building species without disturbing the sediment since adults of all three numerically important tube builders experience mortality after spawning. The manipulation of tube—builder abundances showed that the burrowing species responded to space vacated by tube builders by increased settlement success. Results from experimental variation of A. brevis numbers per unit volume of sediment in the laboratory and abundance data from unmanipulated natural areas also demonstrated the presence of interspecific and intraspecific competition for space. Changes in physical factors due to algal cover had some impact on population levels but the competitive interactions and behavior patterns, revealed only by observations on the behavior of living organisms and manipulation of the infauna, demonstrated the importance of biological interactions to the determination of species abundance patterns in a soft—sediment environment.
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