Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

摘要

DNA contains the instructions required to make proteins and other molecules in cells. DNA is made of four building blocks called deoxyribonucleotides, which are in turn made from molecules called ribonucleotides by enzymes known as ribonucleotide reductases (RNRs for short). RNR enzymes are responsible for maintaining a good balance in the levels of the different deoxyribonucleotides in cells, which is essential for DNA to be made and repaired correctly. Previous work has shown that each RNR can act on all four ribonucleotides. However, these enzymes become more selective for certain ribonucleotides depending on which deoxyribonucleotide is most common within the cell. For example, when a deoxyribonucleotide called dGTP is plentiful, it binds to a so-called “specificity site” on the enzyme and alters the shape of the enzyme’s active site. This then means that a ribonucleotide called ADP will bind in preference to the other ribonucleotides. However, it was not clear how the binding of deoxyribonucleotides to the enzyme influences the shape of the active site. Zimanyi et al. used a technique called X-ray crystallography to determine the three-dimensional structures of a bacterial RNR enzyme when it is bound to all four different combinations of deoxyribonucleotides and ribonucleotides. In the absence of nucleotides, the active site adopts a shape that resembles an open barrel. However, when RNR is bound to a deoxyribonucleotide at the specificity site and a ribonucleotide at the active site, the barrel clamps down, bringing the specificity site and the active site closer together. Additionally, a loop of the protein interacts with each of the deoxyribonucleotides in a different way and communicates their identity directly to the active site, which rearranges itself to hold on to the corresponding preferred ribonucleotide. Zimanyi et al.’s findings provide an explanation for how RNRs can select between ribonucleotides so that they produce a good balance of deoxyribonucleotides in cells. This will inform future efforts to develop molecules that inhibit RNRs, which may have the potential to be used to treat bacterial infections or to kill cancer cells.