Kunishige Kataoka

Structure–function relationships of copper-containing nitrite reductases

Abstract Dissimilatory nitrite reductase (NIR) is a key enzyme in the anaerobic respiratory pathway of denitrifying bacteria. There are two types of NIR, one of which contains copper and the other heme. Cu-containing NIR (Cu NIR) has the trimeric structure with one type 1 Cu (blue copper) atom and one type 2 Cu (nonblue copper) atom in each subunit. The type 1 Cu atom bound by 2His, Cys, and Met accepts one electron from an electron donor protein and shows an intense color, blue or green. The type 2 Cu atom bound by 3His and a solvent (H 2 O or OH − ) is a reduction center of nitrite to NO. The intramolecular long-range electron transfer process is observed from the type 1 site to the type 2 Cu site with a half-life period of ca. 0.3 ms. The present review deals with (i) spectroscopic characterization of Cu NIR’s, (ii) structures of Cu NIR’s, and (iii) functions of Cu NIR’s (intermolecular electron transfer process, intramolecular electron transfer process, and reduction of nitrite ion).

Spectroscopic characterization and intramolecular electron transfer processes of native and type 2 Cu-depleted nitrite reductases

Abstract Native nitrite reductases (NIRs) containing both type 1 and 2 Cu ions and type 2 Cu-depleted (T2D) NIRs from three denitrifying bacteria (Achromobacter cycloclastes IAM 1013, Alcaligenes xylosoxidans NCIB 11015, and Alcaligenes xylosoxidans GIFU 1051) have been characterized by electronic absorption, circular dichroism, and electron paramagnetic resonance spectra. The characteristic visible absorption spectra of these NIRs are due to the type 1 Cu centers, while the type 2 Cu centers hardly contribute in the same region. The intramolecular electron transfer (ET) process from the type 1 Cu to the type 2 Cu in native NIRs has been observed as the reoxidation of the type 1 Cu(I) center by pulse radiolysis, whereas no type 1 Cu in T2D NIRs exhibits the same reoxidation. The ET process obeys first-order kinetics, and observed rate constants are 1400–1900 s–1 (t1/2 = ca. 0.5 ms) at pH 7.0. In the presence of nitrite, the ET process also obeys first-order kinetics, with rate constants decreased by factors of 1/12–1/2 at the same pH. The redox potential of the type 2 Cu site is estimated to be +0.24 - +0.28 V, close to that of the type 1 Cu site. Nitrate and azide ions bound to the type 2 Cu site change the redox potential. Nitrite also would shift the redox potential of the type 2 Cu by coordination, and hence the intramolecular ET rate constant is decreased. Pulse radiolysis experiments on T2D NIRs in the presence of nitrite demonstrate that the type 1 Cu(I) site is slowly oxidized with a first-order rate constant of 0.03 s–1 at pH 7.0, suggesting that nitrite bound to the protein accepts an electron from the type 1 Cu. This result is in accord with the finding that T2D NIRs show enzymatic activities, although they are lower than those of the native enzymes.

Structure of Azurin I from the Denitrifying Bacterium Alcaligenes xylosoxidans NCIMB 11015 at 2.45 Å Resolution

Azurin I from Alcaligenes xylosoxidans NCIMB 11015 (AzN-I) was crystallized by using PEG 4000 as a precipitant. The crystals belong to the monoclinic crystal system and have a space group C2 with the unit-cell parameters of a = 130.67, b = 54.26, c = 74.55 A, and beta = 95.99 degrees. The structure of AzN-I has been solved by the molecular replacement method. Azurin II from the same bacterium (AzN-II) was chosen as the initial structural model. The final crystallographic R value is 17.3% and free R value is 23.6% for 10958 reflections at a resolution of 2.45 A. The root-mean-square deviations for main-chain atoms range between 0.19 and 0.26 A among the four independent molecules in the asymmetric unit. The Cu atom is coordinated to Ndelta of His46 and His117 at 2.0 (1) and 1.9 (1) A, and to Sgamma of Cys112 at 2.2 (1) A, while the carbonyl O atom of Gly45 and Sdelta of Met121 coordinate axially to Cu atom at 2.5 (1) and 3.1 (1) A, respectively. The Cu-N and Cu-S distances of AzN-I are quite similar to those of AzN-II, however, the Cu-SO (Gly45) bond length in AzN-I is 0.25 A shorter than the counterpart in AzN-II. The results have been used to discuss the differences in the spectra of these two proteins.

Spectroscopic and electrochemical properties of the Met86Gln mutant of Achromobacter cycloclastes pseudoazurin

The mutant replacing the Met86 ligand of Achromobacter cycloclastes pseudoazurin (Ac-pAz) with Gln has been prepared and spectroscopically and electrochemically characterized. Ac-pAz has four ligands (2His, Cys, and Met) and donates one electron to its cognate Cu-containing nitrite reductase (Ac-NIR). The mutant ([Met86Gln]pAz) shows the electronic absorption and CD spectra considerably similar to those of zucchini mavicyanin (Mv) and lacquer and cucumber stellacyanins (St) having 2His, Cys, and Gln. The EPR signal of the mutant has an axial character, although those of Mv and St show rhombic signals. The findings indicate that the Cu site having Gln might be a distorted trigonal geometry. The half-wave potentials (E(1/2)) of [Met86Gln]pAz and the intermolecular electron-transfer rate constant (kET) from the mutant to Ac-NIR were determined by cyclic voltammetry at pH 7.0 and 25 degrees C. The E(1/2) is +134 mV (versus NHE) and the coordination of Gln instead of Met negatively shifts the E(1/2) of Ac-pAz (+260 mV (versus NHE)). The kET of [Met86Gln]pAz (1.2x10(6) M(-1) s(-1)) is larger than that of the recombinant Ac-pAz (7.5x10(5) M(-1) s(-1)).

Spectroscopic and electrochemical properties of two azurins (Az-iso1 and Az-iso2) from the obligate methylotroph Methylomonas sp. strain J and the structure of novel Az-iso2.

Methylomonas sp. strain J gives rise to two azurins (Az-iso1 and Az-iso2) with methylamine dehydrogenase (MADH-Mj). The intense blue bands characteristic of Az-iso1 and Az-iso2 are observed at 621 and 616 nm in the visible absorption spectra respectively, being revealed at 620−630 nm in those of usual azurins. The EPR signal of Az-iso1, similar to usual azurins, shows axial symmetry, while the axial EPR signal of Az-iso2 involves a slightly rhombic character. The half-wave potentials (E1/2) of the two azurins and the intermolecular electron-transfer rate constants (kET) from MADH-Mj to each azurin were determined by cyclic voltammetry. The E1/2 values of Az-iso1 and Az-iso2 are +321 and +278 mV vs NHE at pH 7.0, respectively. The kET value of Az-iso2 is larger than that of Az-iso1 by a factor of 5. However, the electron-transfer rate of Az-iso2 is interestingly slower than those of the azurins from a denitrifying bacterium, Alcaligenes xylosoxidans NCIB 11015, and the amicyanin from a different methylotroph, Methylobacterium extorquens AM1. The structure of Az-iso2 has been determined and refined against 1.6 Å X-ray diffraction data. The whole structure of Az-iso2 is quite similar to those of azurins reported already. The Cu(II) site of Az-iso2 is a distorted trigonal bipyramidal geometry like those of other azurins, but some of the Cu-ligand distances and ligand-Cu-ligand bond angle parameters are slightly different. These findings suggest that Az-iso2 is a novel azurin and perhaps functions as an electron acceptor for MADH.

Spectroscopic distinction between two Co(II) ions substituted for types 1 and 2 Cu in nitrite reductase

The Co(II) substitution of nitrite reductases (NIRs) containing types 1 and 2 Cu from two denitrifying bacteria (Achromobactercycloclasters IAM 1013 and Alcaligenes xylosoxidans GIFU 1051) has been carried out. The Co(II) derivatives have been characterized by electronic absorption and magnetic circular dichroism (MCD) spectroscopies. The tetrahedral Co(II) centers replaced type 1 Cu show the MCD bands at 300–500 nm (CysS−aCo(II) charge transfer transitions) and 600–700 nm (d-d transitions of Co(II), which are quite similar to those of Co(II)-substituted plastocyanin. The Co(II) ion will have a donor set of 2His, Cys and Met residues. The enzyme-substituted Co(II) ions for type 2 Cu exhibit the characteristic MCD bands due to d-d transitions in the region of 500–600 nm, which are quite similar to those of half Co(II)-substituted hemocyanin and suggest a tetrahedral Co(II) center bound to three histidyl imidazoles and one water molecule. The two types of Co(II) in NIRs are easily distinguishable by MCD spectroscopy. Moreover, the electronic absorption bands of Co(II) NIRs are assigned to types 1 and 2 Co on the basis of the MCD data.

Crystallization and preliminary X-ray study of iso-2 azurin from the methylotrophic bacterium, Methylomonas J

The obligate methylotroph Methylomonas J possesses two distinct azurins. The iso-2 azurin, which functions as an electron acceptor for methylamine dehydrogenase, has been crystallized using two kinds of precipitants: PEG 4000 and ammonium sulfate. The crystals precipitated with PEG belong to the monoclinic system, space group P21, with unit-cell parameters a = 32.96, b = 33.67, c = 47.34 A and beta = 101.35 degrees. The crystals precipitated with ammonium sulfate belong to the orthorhombic system, space group C2221, with unit-cell parameters a = 31.52, b = 62.49 and c = 135.41 A. The crystals diffract to 1.6 and 1.9 A resolution, respectively, and were suitable for X-ray crystallographic studies. A Patterson search is being conducted using the recently reported structure of Alcaligenes xylosoxidans NCIMB 11015 as a starting model.

MATRIX-ASSISTED LASER DESORPTION/IONIZATION AND ELECTROSPRAY IONIZATION MASS SPECTROMETRY ANALYSIS OF BLUE COPPER PROTEINS. AZURIN AND MAVICYANIN

Two copper proteins azurin-1 and azurin-2 were isolated from denitrifying bacteria Alcaligenes xylosoxidans GIFU1051, and the mass spectrometric analysis of the proteins were carried out by both matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) and electrospray ionization (ESI). The mass spectrometric analysis was also carried out with the recombinant zucchini protein mavicyanin, which was obtained by expression in Escherichia coli. All the proteins were detected as positive ions with the copper atom being eliminated. The molecular weights were determined as 14,017.6 for azurin-1, 13,807.6 for azurin-2 and 11,808.8 for mavicyanin. The observed molecular weight of azurin-1 agrees within two daltons with that calculated from the amino acid composition. Azurin-2 was found to have one different amino acid residue when compared with the known azurin-2 isolated from A. xylosoxidans NCIB11015. The measured molecular weight for the recombinant mavicyanin agrees within two daltons with that of calculated from the amino acid composition of the native protein; therefore, the recombinant mavicyanin is identical to the native protein.

Crystallization and preliminary X-ray crystallographic studies of mavicyanin from Cucurbita pepo medullosa

Mavicyanin isolated from Cucurbita pepo medullosa is a glycosylated protein containing a single polypeptide chain of 109 amino-acid residues and is a member of the phytocyanin subclass of cupredoxins. Non-glycosylated recombinant mavicyanin, which was expressed in Escherichia coli, was crystallized by the hanging-drop vapour-diffusion method with ammonium sulfate as the precipitant at pH 5.5. The crystals belonged to the hexagonal space group P6(1) (or P6(5)), with unit-cell parameters a = 64.0, c = 245.0 A, four molecules per asymmetric unit and a solvent content of 59%. X-ray diffraction data were collected to 1.6 A resolution. To solve the structure of mavicyanin, the MAD method as well as a Patterson search method using the structure of stellacyanin as a starting model are presently being utilized.