Escherichia coli (bacteria)
Ribonucleotide reductases (RNR, also known as Ribonucleoside diphosphate reductase) catalyze the reduction of ribonucleotides to deoxyribonucleotides, the building blocks of DNA, regardless of the base type (A, T, G, C). The reduced groups are the 2' OH-groups of the ribose in the ribonucleotides. Many researchers are attracted to the study of these enzymes because they are essential for DNA synthesis, and because free radicals are involved in their catalytic reactions, making them interesting from a chemist's point of view. Class I RNR consists of two homodimeric proteins, R1 and R2. R1 contains the active site and the substrate-binding site for enzyme reaction, while R2 generates and stores the free radical, the tyrosyl radical Tyr122*, needed for ribonuclease reduction.
The three-dimensional structure of R2 from Escherichia coli determined by X-ray crystallographic analysis and the tyrosyl radicals generated by two experimental methods proposed the mechanism of radical generation and radical transfer. The tyrosyl radical Tyr122* is generated by the cleavage of an oxygen molecule at the diiron center in the R2 protein, and migrates from Tyr122 in R2 to the active-site Cys in R1 in order to catalyze the reduction of ribonucleotides in the R1 protein. This radical transfer induces the catalytic reaction. While the mechanism of radical generation and migration had been revealed, the orientation of tyrosyl radical however was not yet clear, because the crystal structure of R2 containing a tyrosyl radical had not been determined. By using the method of high-field EPR, the structure containing a tyrosyl radical was analyzed. Comparison of the orientation of the radical Tyr122* obtained from high-field EPR with that of the tyrosine Tyr122-OH from crystal structure, reveals a significant conformational change, a rotation of the TYR side chain, away from the diiron center.
Protein Data Bank (PDB)
author: Yuko Tsuchiya