Unusual Trigonal-Planar Copper Configuration Revealed in the Atomic Structure of Yeast Copper−Zinc Superoxide Dismutase^,

Abstract

The three-dimensional structure of yeast copper-zinc superoxide dismutase (CuZnSOD) has been determined in a new crystal form in space group R32 and refined against X-ray diffraction data using difference Fourier and restrained crystallographic refinement techniques. The unexpected result is that the copper ion has moved approximately 1 angstrom from its position in previously reported CuZnSOD models, the copper-imidazolate bridge is broken, and a roughly trigonal planar ligand geometry characteristic of Cu(I) rather than Cu(II) is revealed. Final R values for the two nearly identical room temperature structures are 18.6% for all 19 149 reflections in the 10.0-1.7 angstrom resolution range and 18. 2% for 17 682 reflections (F > 2 sigma) in the 10.0-1.73 angstrom resolution range. A third structure has been determined using X-ray data collected at -180 degrees C. The final R value for this structure is 19.0% (R(free) = 22.9%) for all 24 356 reflections in the 10.0-1.55 angstrom resolution range. Virtually no change in the positions of the ligands to the zinc center is observed in these models. The origin of the broken bridge and altered Cu-ligand geometry is discussed.

The solution structure of reduced dimeric copper zinc superoxide dismutase. The structural effects of dimerization

“…In the reduced state, the bond between Cu and His63 is broken, producing an increase in distance between the two. In the case of the reduced dimeric yeast enzyme this distance increases to 3.2 Å [20]. In the present structure the reduced copper is clearly tricoordinated, as expected from the data on the monomer.…”

“…The X-ray structure of the oxidized form has been available since 1982 for the bovine enzyme [6,7] and several other structures have become available [8][9][10][11][12][13][14][15][16][17][18]. Reduced state structures are also available although the picture is less clear-cut around the copper-binding site [19][20][21]. Certainties on the protonation of His63, which bridges Cu and Zn in the oxidized form but is protonated in the reduced form, come from 1 H NMR studies [22][23][24][25].…”

Long Distance Charge Redistribution Upon Cu,Zn-Superoxide Dismutase Reduction

“…A main result concerns the rupture of the interaction between reduced Cu(I) and the His-63 bridging ligand, as deduced by NMR (10,(23)(24)(25), extended X-ray absorption fluorescence spectroscopy (26,27), and Raman spectroscopy (28 -30) for Cu,Zn-SOD in solution. Three-dimensional crystallographic structures of reduced Cu,Zn-SOD presented heterogeneity of the active center (16,(31)(32)(33), but a recent high resolution structure provided convincing evidence for three coordinated Cu(I) (34), in agreement with other spectroscopic data.…”

“…Structural factors at the origin of this specific and efficient dismutase mechanism are not fully understood. Thorough analyses at the molecular level of structural changes that accompany copper reduction have been undertaken to detail the active site properties at the origin of the efficient superoxide dismutation and of the protonation events associated with its reduction into hydrogen peroxide (3,5,10,(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34). A main result concerns the rupture of the interaction between reduced Cu(I) and the His-63 bridging ligand, as deduced by NMR (10,(23)(24)(25), extended X-ray absorption fluorescence spectroscopy (26,27), and Raman spectroscopy (28 -30) for Cu,Zn-SOD in solution.…”

Catalytic Roles for Two Water Bridged Residues (Asp-98 and His-255) in the Active Site of Copper-containing Nitrite Reductase

“…A catalytic role for His-255 has been suggested from a comparison to the SOD copper center that is ligated by four histidine ligands in a plane and a water molecule in the apical position (18). The recent crystal structure of the reduced yeast SOD (19) demonstrates a structural rearrangement following protonation of a histidine ligand (His-63) resulting in a more tetrahedral coordination of the copper similar to that found in AxNIR (14). As a result, His-63 adopts a position structurally analogous to His-249 in AxNIR and His-255 in AfNIR.…”