Z. H. L. Abraham

The intramolecular electron transfer between copper sites of nitrite reductase: a comparison with ascorbate oxidase

The intramolecular electron transfer (ET) between the type 1 Cu(I) and the type 2 Cu(II) sites of Alcaligenes xylosoxidans dissimilatory nitrite reductase (AxNiR) has been studied in order to compare it with the analogous process taking place in ascorbate oxidase (AO). This internal process is induced following reduction of the type 1 Cu(II) by radicals produced by pulse radiolysis. The reversible ET reaction proceeds with a rate constant k ET=k 1→2+k 2→1 of 450±30 s−1 at pH 7.0 and 298 K. The equilibrium constant K was determined to be 0.7 at 298 K from which the individual rate constants for the forward and backward reactions were calculated to be: k 1→2=185±12 s−1 and k 2→1265±18 s−1. The temperature dependence of K allowed us to determine the ΔH° value of the ET equilibrium to be 12.1 kJ mol−1. Measurements of the temperature dependence of the ET process yielded the following activation parameters: forward reaction, ΔH ≠=22.7±3.4 kJ mol−1 and ΔS ≠=−126±11 J K−1 mol−1; backward reaction, ΔH ≠=10.6±1.7 kJ mol−1 and ΔS ≠=−164±15 J K−1 mol−1. X‐ray crystallographic studies of NiRs suggest that the most probable ET pathway linking the two copper sites consists of Cys136, which provides the thiolate ligand to the type 1 copper ion, and the adjacent His135 residue with its imidazole being one of the ligands to the type 2 Cu ion. This pathway is essentially identical to that operating between the type 1 Cu(I) and the trinuclear copper centre in ascorbate oxidase, and the characteristics of the internal ET processes of these enzymes are compared. The data are consistent with the faster ET observed in nitrite reductase arising from a more advantageous entropy of activation when compared with ascorbate oxidase.

The substrate-binding site in Cu nitrite reductase and its similarity to Zn carbonic anhydrase.

Here we investigate the structure of the two types of copper site in nitrite reductase from Alcaligenes xylosoxidans, the molecular organisation of the enzyme when the type-2 copper is absent, and its mode of substrate binding. X-ray absorption studies provide evidence for a fourth ligand at the type-2 Cu, that substrate binds to this site and indicates that this binding does not change the type-1 Cu centre. The substrate replaces a putative water ligand and is accommodated by a lengthening of the Cu–histidine bond by approximately 0.08 Å. Modelling suggests a similarity between this unusual type-2 Cu site and the Zn site in carbonic anhydrase and that nitrite is anchored by hydrogen bonds to an unligated histidine present in the type-2 Cu cavity.

Structures of oxidized and reduced azurin II from Alcaligenes xylosoxidans at 1.75 Å resolution

Crystallographic structures of oxidized and reduced forms of azurin II are reported at 1.75 A resolution. Data were collected using one crystal in each case and by translating the crystal after each oscillation range to minimize photoreduction. Very small differences are observed at the Cu site upon reduction and these cannot be determined with confidence at current resolution. A comparison with the three-dimensional EXAFS reveals a good correspondence for all the ligand distances except for Cu-His46, where a larger deviation of approximately 0.12-0.18 A is observed, indicating that this ligand is more tightly restrained in the crystallographic refinement at the current resolution.

Structure Solution of Azurin II from Alcaligenes xylosoxidans using the Laue Method: Possibility of Studying In Situ Redox Changes using X-rays.

We have recently demonstrated that X-rays can be used for changing the redox states of the metal centre in metalloproteins [Murphy et al. (1995). J. Synchrotron Rad. 2, 64-69]. The possibility of using the Laue method for studying the structural changes associated with such X-ray-induced reactions is explored by applying the method to the structure determination of a new azurin (hereafter referred to as azurin II) from the denitrifying bacterium Alcaligenes xylosoxidans. Laue X-ray diffraction data of azurin II were collected at station 9.7 of the SRS Daresbury. Three diffraction patterns were recorded on film packs at three different crystal orientations. The data were processed using the Daresbury Laue Software Suite to give 2224 independent single reflections (R(merge) = 0.136) in the wavelength range 0.36-1.40 A. The data completeness was 44% at 2.55 A resolution. Phase determination for the data was undertaken using the molecular-replacement method; the top peak was chosen in both the rotation function and the subsequent translation function. This solution agreed well with the molecular-replacement solution achieved independently using monochromatic data. The electron-density map showed reasonably good agreement with the model and the copper site was readily recognizable as it had the highest density. To see if the electron-density map could be improved, ;the doublets in the diffraction data were then deconvoluted. This added 26% data in the region infinity-2d(min) resulting in an improvement in the data completeness to 50% and thus in improved continuity of the electron-density map. The quality of these maps is discussed from the point of view of the suitability of this approach for studying redox-induced structural changes.

Crystallographic Structures of Nitrite Reductase and its Substrate Bound Complex

Dissimilatory nitrite reductase (NiR) is a key enzyme in the anaerobic respiratory pathway of denitrifying bacteria where nitrate is sequentially reduced to the gaseous products NO, N2O or N2, leading to a significant loss of fixed nitrogen from the terrestrial environment (Payne, 1985). The NiR from Alcaligenes xylosoxidans (AxNiR) (Abraham et al., 1993) belongs to the group of NiRs which utilise copper at the redox active centres. All Cu NiRs isolated so far have a strong band near 600nm arising from a (Cys)S → Cu (II) charge transfer which is characteristic of a type 1 Cu centre. The ratio of intensity of this band to a second charge transfer absorption band at ∼460nm determines whether a Cu NiR is blue or green in colour (Han et al., 1993). AxNiR belongs to the subset of Cu-NiRs which are blue in colour and are thought to have azurin as the electron partner.