Dissimilatory Nitrite and Nitric Oxide Reductases

Averill, Bruce A.

doi:10.1021/cr950056p

Cited by 503 publications

(597 citation statements)

References 133 publications

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“…Proteomics confirmed the ACD10 and ACD23 nirS proteins were synthesized in situ (Supplementary Table S1). However, given proteomic evidence for nitrite reductase only, it is possible these proteins may have other functions, including the detoxification or reduction of oxygen or sulfite (Averill, 1996;Pereira et al, 2000).…”

Section: Metabolic Interdependencies In An Aquifer Microbial Communitmentioning

confidence: 99%

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

et al. 2014

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Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via acetate amendment of the groundwater occurring over 2 successive years. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include organisms from a new phylum, Melainabacteria, most closely related to Cyanobacteria, phylogenetically novel members of the Chloroflexi and Bacteroidales, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen metabolism in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate and iron reduction. Thus, fermentation carried out by previously unknown members of sediment microbial communities may be an important driver of nitrogen, hydrogen, sulfur, carbon and iron cycling.

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Section: Metabolic Interdependencies In An Aquifer Microbial Communitmentioning

confidence: 99%

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

et al. 2014

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“…The steps in the mechanism of nitrite reduction by CuNiRs involves the binding of HNO 2 to the oxidized enzyme, reduction and dehydration of bound intermediates, followed by the release of the product NO to reform the oxidized enzyme (30). Even though the origin of the nitrite and NO-bound adducts harvested via high-throughput crystal structure determination is unclear, it is evident that they represent substrate͞product adducts of AcNiR that have remained essentially stable (product in Scheme 1D) because of the curtailment of enzyme turnover under conditions used for the isolation of the enzyme.…”

Section: Structure Of Endogenously Bound Nitrite and No In The Samementioning

confidence: 99%

Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism

Antonyuk

Strange

Sawers

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

174

258

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Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using ''crystal harvesting'' and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 Å, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 Å and 1.15 Å, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 Å resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.catalysis ͉ denitrification ͉ enzyme mechanism ͉ nitrite and nitric oxide binding ͉ crystal structures

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“…Although gross comparison between properties measured on immobilized and freely diffusing biomolecules tends to show good agreement (1,3), more subtle aspects of biomolecule behavior such as property distribution widths and shapes (6, 7) and conformational dynamics (6,8) have been shown to be affected by immobilization, and in some cases, immobilization has been suspected of contributing to observed enzyme behavioral heterogeneity (4). In this report we take an important step toward viewing the richness of single-enzyme dynamics without immobilization by making observations of multiple turnover events of single solution-phase molecules of a blue nitrite reductase (bNiR), an important redox-active enzyme in bacterial denitrification (9).…”

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confidence: 99%

“…bNiR is a multicopper enzyme that carries out the one-electron reduction of nitrite, NO 2 − , to nitric oxide, NO, in the presence of a suitable reductant (9). It is a trimer, 10 nm in diameter, and contains two different Cu sites (13).…”

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confidence: 99%

Redox cycling and kinetic analysis of single molecules of solution-phase nitrite reductase

Goldsmith

Tabares

Kostrz

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Single-molecule measurements are a valuable tool for revealing details of enzyme mechanisms by enabling observation of unsynchronized behavior. However, this approach often requires immobilizing the enzyme on a substrate, a process which may alter enzyme behavior. We apply a microfluidic trapping device to allow, for the first time, prolonged solution-phase measurement of single enzymes in solution. Individual redox events are observed for single molecules of a blue nitrite reductase and are used to extract the microscopic kinetic parameters of the proposed catalytic cycle. Changes in parameters as a function of substrate concentration are consistent with a random sequential substrate binding mechanism.ABEL trap | enzymology | electron transfer | fluorescence | catalysis M easurements made on the activity of single enzymes have revolutionized the picture of these molecular machines' mode of operation by providing evidence for static and dynamic heterogeneity, enabling the observation of transient intermediates, and allowing determination of the microscopic rate constants comprising complex catalytic cycles under turnover conditions (1-4). However, conclusions regarding enzyme dynamics require the observation of multiple turnovers of a single molecule with a requisite observation window of several seconds or more. Because this window is several orders of magnitude longer than the typical dwell time of a solution-phase molecule diffusing through a confocal detection volume, molecules that naturally exist in solution are often immobilized on a solid support (1-3, 5). Although gross comparison between properties measured on immobilized and freely diffusing biomolecules tends to show good agreement (1, 3), more subtle aspects of biomolecule behavior such as property distribution widths and shapes (6, 7) and conformational dynamics (6, 8) have been shown to be affected by immobilization, and in some cases, immobilization has been suspected of contributing to observed enzyme behavioral heterogeneity (4). In this report we take an important step toward viewing the richness of single-enzyme dynamics without immobilization by making observations of multiple turnover events of single solution-phase molecules of a blue nitrite reductase (bNiR), an important redox-active enzyme in bacterial denitrification (9).Prolonged solution-phase measurements are enabled through use of a specialized microfluidic trapping device that cancels the Brownian motion of a single emissive solution-phase object through the use of directed electroosmotic forces, the anti-Brownian electrokinetic (ABEL) trap (10, 11). The ABEL trap estimates particle position via a revolving laser spot phase-locked in a homebuilt analogue circuit to a restoring force gated by photon detection and applied via two orthogonal pairs of electrodes (11). This scheme results in the confinement of the object in a spatially homogeneous excitation volume for multiple seconds without immobilization and can be applied to single biomolecules substantially smaller than the large...

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Dissimilatory Nitrite and Nitric Oxide Reductases

Cited by 503 publications

References 133 publications

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism

Redox cycling and kinetic analysis of single molecules of solution-phase nitrite reductase

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