Nitrite copper site

The nature of the copper in these proteins is not totally clear. Dooley et al (1988) reported that the Achromobacter protein may have two kinds of type I sites in a total of three copper sites per dimeric protein, while the A. faecalis protein was reported to be a tetrameric protein with both type I and type II coppers (KakutanielaZ., 1981). Interestingly, the Achromobacter protein is green. Both of these nitrite reductases accept electrons from a cupredoxin. 

Arrangement of subunits in nitrite reductase from Achromohacter cycloclastes. Domains are denoted D1 and D2, copper sites are shaded spheres, and Cu ligands are denoted by one-letter abbreviations C for cysteine sulfur and H for histidine imidazole nitrogen. From Fenderson et al. (1991). 

Sano, M., and Matsubara, T. (1988). Structural change in the one-electron oxidation-reduction at the copper site in nitrite reductase. Evidence from EXAFS. Inorg. Chem. Acta Bioinorg. Chem 152, 53-54. 

Fig. 5-13. Copper site of nitrite reductase form A. cyclocastes.

The classification introduced in this review (type I-type IV) should cover all structural types of copper sites known to date. For instance, based on this nomenclature, ascorbate oxidase contains type I and type IV, and nitrite reductase contains type I and type II (more precisely, type IIA). Galactose oxidase has a type IIB site. 

The crystal structure of nitrite reductase (NiR) from Achromobacter cycloclastes was recently reported by Godden et al. (46). The protein contains both a type I and a type II copper site. The type I center has a distorted tetrahedral structure typical of type I copper, whereas the... 

Figure 1. Schematic representation of the copper sites in nitrite reductase from Achromobacter cycloclastes (17).

Theoretically, the redox potential of the type 1 Cu(II) could provide the specificity toward a particular reductive substrate in comparison to another. Type 1 copper sites do exhibit a remarkable variability in reduction potential, from 240 mV in nitrite reductase (LaCroix et al., 1996 Suzuki et al., 1994) to >1 V for a noncatalytic type 1 copper in hCp (Machonkin et al., 1998). This variability is certainly due in part to the presence of the methionine ligand found in the four-coordinate type 1 site (as in hCp and AO) that is absent in Lac and FetSp, for example (cf. Figs. 1 and 12). Mutagenesis studies indicate that this ligand tunes ... 

Intriguingly, the blue copper sites, especiaUy those with a carbonyl oxygen at the axial coordination position, display high affinity for Zn + ions. Mutants in which the Met is replaced by Gin or Glu preferentiaUy bind Zn + when expressed in heterologous systems, e.g., Escherichia coli. Examples include azurin, amicyanin, nitrite reductase, and possibly also plastocyanin (Diederix et al., 2000 Hibino et al., 1995 Murphy et al., 1995 Nar et al., 1992a Romero et al., 1993). In the case of azurin it has been shown that both wild-type and the Met—Gin mutant have the same affinity for both Zn +and Cu + (Romero ci a/., 1993). In addition, EXAFS studies showed that some preparations of blue copper proteins purihed from their natural sources also contain small fractions of Zn derivatives (DeBeer George, personal communication). 

Dodd, F. E., van Beeumen, J., Eady, R. R., and Hasnain, S. S., 1998, X-ray structure of a blue copper nitrite reductase in two crystal forms. The nature of the copper sites, mode of substrate binding and recognition by redox partner, J. Mol. Biol. 282 3699382. 

Figure 14 Similarity between the putative electron-transfer routes to and from the type 1 copper sites in plastocyanin and nitrite reductase. (Reproduced with permission of Chapman and Hall from J. Sanders-Loehr, in Bioinorganic Chemistry of Copper , ed. K.D. Karlin and Z. Tyeklar, 1993, p. 51) ...

The physiological electron donors for NIR are either the cupredoxins pseudoazurin or azurin depending on the organism. Pseudoazurin, for example, reduces the type-1 copper and subsequently the electron is transferred to the type-2 copper site, which is also the binding site for nitrite. Nitrite is bound to the type-2 copper site as demonstrated by electron nucleus double resonance studies on NIR from Achromohacter xylosoxidans and in a crystal structure of the complex between nitrite and NIR from A. cycloclastes The crystal structure of the complex shows that nitrite binds asymmetrically with the oxygens toward the copper. 

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