Type 1 Cu Structure of Blue Nitrite Reductase from Alcaligenes xylosoxidans GIFU 1051 at 2.05   Resolution: Comparison of Blue and Green Nitrite Reductases

Inoue, Tsuyoshi; Gotowda, M.; Deligeer,; Kataoka, Keisuke; Yamaguchi, Kazuya; Suzuki, Shinnichiro; Watanabe, Hirotaka; Gohow, M.; Kai, Yasushi

doi:10.1093/oxfordjournals.jbchem.a022201

Cited by 79 publications

(62 citation statements)

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“…Copper-containing nitrite reductases present a trimeric structure [43][44][45][46] and contain both type 1 (T1Cu) and type 2 (T2Cu) copper centers (Fig. 3).…”

Section: Copper Nitrite Reductase (Cunir)mentioning

confidence: 99%

Metalloenzymes of the denitrification pathway

Tavares

Pereira

Moura

et al. 2006

Journal of Inorganic Biochemistry

199

148

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“…Copper-containing nitrite reductases present a trimeric structure [43][44][45][46] and contain both type 1 (T1Cu) and type 2 (T2Cu) copper centers (Fig. 3).…”

Section: Copper Nitrite Reductase (Cunir)mentioning

confidence: 99%

Metalloenzymes of the denitrification pathway

Tavares

Pereira

Moura

et al. 2006

Journal of Inorganic Biochemistry

199

148

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“…NiR reduces nitrite to produce NO (g) , and NO reductase reduces NO to N 2 O, where NO is the first gaseous compound in the pathway. 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).…”

mentioning

confidence: 99%

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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“…There are two main categories of NIR: the hemecontaining and Cu-containing enzymes (1). Generally, Cucontaining NIRs (CuNIRs) from Achromobacter cycloclastes (green AcNIR) (4,5), Alcaligenes faecalis (green AfNIR) (5,6), and Alcaligenes xylosoxidans (blue AxNIR) (5,7,8) fold a trimeric structure in which a monomer (Ϸ37 kDa) contains one type 1 Cu and one type 2 Cu. The monomer is composed of two consecutive Greek key ␤-barrel folding domains.…”

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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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Type 1 Cu Structure of Blue Nitrite Reductase from Alcaligenes xylosoxidans GIFU 1051 at 2.05 Resolution: Comparison of Blue and Green Nitrite Reductases

Cited by 79 publications

References 0 publications

Metalloenzymes of the denitrification pathway

Metalloenzymes of the denitrification pathway

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

Structure and function of a hexameric copper-containing nitrite reductase

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