Structure–function relationships of copper-containing nitrite reductases

Suzuki, Shinnichiro; Kataoka, Keisuke; Yamaguchi, Kazuya; Inoue, Tsuyoshi

doi:10.1016/s0010-8545(99)00069-7

Cited by 99 publications

(105 citation statements)

References 68 publications

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“…This may contribute to the rapid decrease in enzyme activity as the pH is increased from 6.0 to 9.0 (23,24). Similar conclusions were drawn from studies of the change in type 2 copper site reduction potential in the Cu-NiRs from A. xylosoxidans and A. cycloclastes (1). From our structural data, an explanation for the observed decrease in redox potential of the type 2 copper site at higher pH can be hypothesized.…”

Section: Resultssupporting

confidence: 84%

“…The reduction potential of the type 2 copper site is crucial for the activity of the protein, since a lower reduction potential of the type 2 copper site relative to that of the type 1 copper site retards electron transfer. Previous measurements have led to the conclusion that the reduction potential of the type 2 copper site in RsNiR is among the lowest observed for Cu-NiRs (1,9) and that nitrite binding to the type 2 copper site is needed to shift the balance of the copper site reduction potentials so as to allow electron transfer (9). Because pH-dependent changes in geometry were observed in our structures, we determined the reduction potential of the type 2 copper site using EPR at pH 6.0 and 8.4 by recording a full redox titration under anaerobic conditions.…”

Section: Resultsmentioning

confidence: 99%

“…The nitrogen cycle has received much attention in recent years due to the fact that several substrates and products of the pathway are known to be environmental pollutants (1). In dissimilatory denitrification (2), nitrate is used as an alternative electron acceptor during respiration when oxygen is scarce, being reduced stepwise and finally returned to the biosphere as inorganic nitrogen.…”

mentioning

confidence: 99%

“…There are two main categories of NiRs; those that are heme-containing (cd1-NiRs) (3,4) and those that are copper-containing (Cu-NiRs) (5)(6)(7)(8). The overall enzymatic reaction performed by NiRs is NO 2 Ϫ ϩ 2H ϩ ϩ e Ϫ 3 NO (g) ϩ H 2 O. Cu-NiRs are blue or green in color, showing visible absorption at 460 and 600 nm (1). The relative magnitude of these absorption peaks determines the enzyme color (i.e.…”

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confidence: 99%

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pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Jacobson

Pistorius

Farkas

et al. 2007

Journal of Biological Chemistry

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Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

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Section: Resultssupporting

confidence: 84%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Jacobson

Pistorius

Farkas

et al. 2007

Journal of Biological Chemistry

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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%

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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Copper Nitrite Reductase

Adman

Murphy

2004

Handbook of Metalloproteins

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Copper nitrite reductase catalyzes the one electron reduction of nitrite to nitric oxide as part of the dissimilatory denitrification pathway. Copper nitrite reductases are found in some fungi and archaea and in many divisions of bacteria. The crystal structure of the enzyme reveals a homotrimer, each of which has a type 1 Cu site that mediates electron transfer to a type 2 Cu site. The three type 2 Cu sites are found at the subunit interfaces and catalyze nitrite reduction. Extensive mutagenic, spectroscopic, kinetic, and crystallographic studies have explored the catalytic mechanism that is proposed to include a copper–nitrosyl intermediate.

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Structure–function relationships of copper-containing nitrite reductases

Cited by 99 publications

References 68 publications

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Structure and function of a hexameric copper-containing nitrite reductase

Copper Nitrite Reductase

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