Structure of a new azurin from the denitrifying bacterium Alcaligenes xylosoxidans at high resolution

It has been reported previously that Alcaligenes xylosoxidans (NC1MB 11015) grown under denitrifying conditions produces two azurins instead of the single previously identified azurin [Dodd, Hasnain, Hunter, Abraham, Debenham, Kanzler, Eldridge, Eady, Ambler & Smith (1995). Biochemistry. In the press]. The new azurin, called azurin II, has been crystallized as blue elongated rectangular prisms with the tetragonal space group P4₁22 and unit-cell parameters a = b = 52.65, c = 100.63 Å. X-ray crystallographic data extending to 1.9 Å resolution were collected by the Weissenberg method using 200 × 400 mm image plates and synchrotron X-rays of wavelength 0.97 Å. The three-dimensional structure of azurin II has been solved by the molecular-replacement method using the structure of azurin from Alcaligenes denitrificans NCTC 8582 with which this new azurin shows a close homology. The quality of the initial map was sufficient to predict a number of sequence differences. The model is currently refined to an R-factor of 18.8% with X-ray data between 8.5 and 1.9 Å. The final model of 961 protein atoms, one Cu atom and 50 water molecules has r.m.s. deviations from ideality of 0.009 Å for bond lengths and 1.7° for bond angles. The overall structure is similar to that of the azurin from A. denitrificans NCTC 8582. It has a β-barrel structure with the Cu atom located near the top end of the molecule. The Cu atom is coordinated to Nδ of His46 and His117 at 2.02 Å and to Sγ of Cys112 at 2.12 Å, while the carbonyl O atom of Gly45 and Sδ atom of Met121 provide the additional interactions at 2.75 and 3.26 Å, respectively.