Structure of Nitrite Bound to Copper-containing Nitrite Reductase from Alcaligenes faecalis

Murphy, M.E.P.; Turley, S.; Adman, Elinor T.

doi:10.1074/jbc.272.45.28455

Cited by 205 publications

(276 citation statements)

References 37 publications

(42 reference statements)

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“…For the green nitrite reductases, resolution of the structure has steadily improved with the highest resolution being 1.4 Å. The nature of substrate binding in CuNiRs has been the focus of a number of biochemical, spectroscopic (electron nuclear double resonance͞x-ray absorption fine structure), and crystallographic studies (10,13,14,(16)(17)(18)(19). These studies have been in general agreement that nitrite binds to the T2Cu ion via O in an asymmetric bidentate fashion.…”

mentioning

confidence: 54%

“…X-ray crystal structures have been determined for the green NiRs from Achromobacter cycloclastes (AcNiR) (9,10) and Alcaligenes faecalis NiR (4,(11)(12)(13) and the blue Alcaligenes xylosoxidans (AxNiR) (14,15), for which an atomic resolution structure has been reported recently (5). For the green nitrite reductases, resolution of the structure has steadily improved with the highest resolution being 1.4 Å.…”

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confidence: 99%

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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.

169

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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confidence: 54%

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.

169

258

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“…Nitrite binds directly to the type 2 copper ion (14), with both oxygen atoms ligating the copper site in a bidentate fashion (6,13). After an electron is passed to the type 1 copper site from the electron donor protein, the electron is transferred on to nitrite via the type 2 copper ion (15).…”

mentioning

confidence: 99%

“…The type 2 copper site is situated at the monomer-monomer interfaces and has ligands from both monomers (His A131, His A166, His B338), forming a propeller-shaped structure with the copper at its center. When the type 2 copper is oxidized, there is also a fourth ligand, a solvent molecule, but this ligand disorders upon reduction of the type 2 copper ion (12,13).…”

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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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Structure of Nitrite Bound to Copper-containing Nitrite Reductase from Alcaligenes faecalis

Cited by 205 publications

References 37 publications

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

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

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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