Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase

• DOI: 10.1021/jacs.0c04325
• Publication Date: 2020-07-07T05:48:35Z
• Authors: Clorice R. Reinhardt; Pengfei Li; Gyunghoon Kang; JoAnne Stubbe; Catherine L. Drennan; Sharon Hammes-Sch...
• Keywords: Ribonucleotide reductase; Proton-Coupled Electron Transfer; Ribonucleotide; Acceptor

Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in organisms. The active form E. coli Ia RNR is composed two homodimers that α2β2 complex. Catalysis initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β Y731α at interface. Resolving PCET α/β interface has been long-standing challenge due lack structural data. Herein, molecular dynamics simulations based on recently solved cryogenic-electron microscopy structure an complex performed examine fluctuations interfacial water, as well hydrogen-bonding interactions conformational motions residues along pathway. Our free energy reveal Y731 able sample both flipped-out conformation, where it points toward facilitate with Y356, stacked conformation Y730 enable collinear this residue. Y356 exhibit water molecules and, some conformations, share bridging molecule, suggesting primary proton acceptor from water. flexibility hydrogen-bonded chains appear critical effective These consistent biochemical spectroscopic data provide previously unattainable atomic-level insights into fundamental mechanism RNR.