Metal Coordination and Mechanism of Multicopper Nitrite Reductase

Suzuki, Shinnichiro; Kataoka, Keisuke; Yamaguchi, Kazuya

doi:10.1021/ar9900257

Cited by 154 publications

(167 citation statements)

References 52 publications

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“…This indicates that electron transfer from type I Cu to the Cu ion accommodated in the trinucelar center and following oxidation with dioxygen are possible. This situation is similar to the reaction process of Cunitrite reductase containing two Cu ions [type I Cu and type II Cu (positioned at the site corresponding to type III Cu)], in that the intramolecular electron transfer from type I Cu is gated by the state of the type II Cu site (23). The His456.458Val mutant contained only one Cu ion at the type I Cu site, and did not show BO and ferroxidase activities, although the reduced type I Cu was easily oxidized through the action of hexacyanoferrate (III) to give a spectrum similar to those shown by plastocyanin and azurin without a shoulder at 330 nm.…”

Section: His456458lys Mutant-mentioning

confidence: 77%

Type III Cu Mutants of Myrothecium verrucaria Bilirubin Oxidase

Shimizu¹

2003

Journal of Biochemistry

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Type III Cu ligand, His456 and His458, of Myrothecium verrucaria (MT-1) bilirubin oxidases (BO) [EC 1.3.3.5] were doubly mutated as to Lys, Asp, and Val. In spite of perturbation of the type III Cu centers, these mutants were pale blue or colourless when isolated. However, they became intense blue on reaction with reducing agents such as dithionite, ascorbate, hexacyanoferrate(II), and octacyanotangstate(IV) under air, or with an oxidizing agent such as hexacyanoferrate(III), indicating that they are in mixed forms when expressed in Aspergillus oryzae. His456.458Lys and His456.458Asp mutated as to potential coordinating groups showed weak BO and ferroxidase activities, while His 456.458Val mutated as to non-coordinating groups showed no enzyme activity at all.

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Section: His456458lys Mutant-mentioning

confidence: 77%

Type III Cu Mutants of Myrothecium verrucaria Bilirubin Oxidase

Shimizu¹

2003

Journal of Biochemistry

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“…It has agronomic, environmental, and medical impacts (1)(2)(3). The individual reactions of denitrification are catalyzed by distinct reductases that variously contain Mo, Fe, Cu, or heme centers.…”

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confidence: 99%

“…The reduction of nitrite to NO is catalyzed by nitrite reductase (NiR). Bacteria employ one of two different forms of NiR, containing either heme cd 1 -or Cu in their prosthetic group (2,3). Cu-nitrite reductases are divided into two subclasses based on their colors, green and blue, and their redox partners, pseudoazurin and azurin, respectively.…”

mentioning

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.

170

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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“…denitrification ͉ electron transfer ͉ redox partner ͉ intermolecular interaction ͉ cupredoxin T he terrestrial nitrogen cycle sustained by some bacteria plays an important role in all organism kingdoms (1)(2)(3). Inorganic nitrogen is introduced into the biosphere by the biological fixation of atmospheric dinitrogen to produce NH 3 and is removed through the process of denitrification.…”

mentioning

confidence: 99%

“…Inorganic nitrogen is introduced into the biosphere by the biological fixation of atmospheric dinitrogen to produce NH 3 and is removed through the process of denitrification. During the mutual conversion of NH 3 , NO 3 Ϫ , and NO 2 Ϫ by bacteria, inorganic nitrogen is changed into the organic nitrogen required by all organisms. Finally NO 3 Ϫ or NO 2 Ϫ is reduced to dinitrogen via the gaseous nitrogen oxides, NO and N 2 O, by dissimilatory denitrification.…”

mentioning

confidence: 99%

Structure and function of a hexameric copper-containing nitrite reductase

Nojiri

Xie

Inoue

et al. 2007

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

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Dissimilatory nitrite reductase (NIR) is a key enzyme in denitrification, catalyzing the first step that leads to gaseous products (NO, N 2O, and N2). We have determined the crystal structure of a Cu-containing NIR from a methylotrophic denitrifying bacterium, Hyphomicrobium denitrificans, at 2.2-Å resolution. The overall structure of this H. denitrificans NIR reveals a trigonal prism-shaped molecule in which a monomer consisting of 447 residues and three Cu atoms is organized into a unique hexamer (i.e., a tightly associated dimer of trimers). Each monomer is composed of an N-terminal region containing a Greek key ␤-barrel folding domain, cupredoxin domain I, and a C-terminal region containing cupredoxin domains II and III. Both cupredoxin domains I and II bind one type 1 Cu and are combined with a long loop comprising 31 amino acid residues. The type 2 Cu is ligated at the interface between domain II of one monomer and domain III of an adjacent monomer. Between the two trimeric C-terminal regions are three interfaces formed by an interaction between the domains I, and the type 1 Cu in the domain is required for dimerization of the trimer. The type 1 Cu in domain II functions as an electron acceptor from an electron donor protein and then transfers an electron to the type 2 Cu, binding the substrate to reduce nitrite to NO. The discussion of the intermolecular electron transfer process from cytochrome c 550 to the H. denitrificans NIR is based on x-ray crystallographic and kinetic results.denitrification ͉ electron transfer ͉ redox partner ͉ intermolecular interaction ͉ cupredoxin

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Metal Coordination and Mechanism of Multicopper Nitrite Reductase

Cited by 154 publications

References 52 publications

Type III Cu Mutants of Myrothecium verrucaria Bilirubin Oxidase

Type III Cu Mutants of Myrothecium verrucaria Bilirubin Oxidase

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

Structure and function of a hexameric copper-containing nitrite reductase

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