Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer

The R2 subunits of class I ribonucleotide reductases (RNRs) house a diferri c-tyrosyl radical (Y-.) cofactor essential for DNA synthesis. in yeast, the re are two R2 proteins, Y2 and Y4. Although both Y2 and Y4 are homologous t o 112s from other organisms, Y4 lacks three conserved iron-binding residues , and its exact function is unclear. Y4 is required for assembly of the dif erric-Y-. cofactor in Y2, and the two proteins can form both homodimeric an d heterodimeric complexes. The Y2Y4 heterodimer was crystallized from a mix ture of the two proteins, and its structure was determined to 2.8 A resolut ion. Both Y2 and Y4 are completely a helical and resemble the mouse and Esc herichia coil 112s in overall fold. Three alpha helices. not observed in th e mouse R2 structure are present at the Y2 N terminus, and one extra N-term inal helix is observed in Y4. In addition, one of the eight principal helic es in both Y2 and Y4, alphaD, is shifted significantly from its position in mouse R2. The heterodimer interface is similar to the mouse R2 homodimer i nterface in size and interacting residues, but loop regions at the interfac e edges differ. A single metal ion, assigned as Zn(II), occupies the Fe2 po sition in the Y2 active site. Treatment of the crystals with Fe(II) results in difference electron density consistent with formation of a diiron cente r. No metal-binding site is observed in Y4. Instead, the residues in the ac tive site region form a hydrogen-bonding network involving an arginine, two glutamic acids, and a water molecule.