Active site structure of class I ribonucleotide reductase intermediate X: a density functional theory analysis of structure, energetics, and spectroscopy.
Several models for the active site structure of class I ribonucleotide reductase (RNR) intermediate X have been studied in the work described in this paper, using broken-symmetry density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model. The calculated properties, including geometries, spin states, 57Fe, 1H, and 17O hyperfine tensors, Mössbauer isomer shifts, and quadrupole splittings, and the estimation of the Fe(IV) d-d transition energies have been compared with the available experimental values. On the basis of the detailed analysis and comparisons, we propose a definite form for the active site structure of class I RNR intermediate X, which contains an Fe1(III)Fe2(IV) center (where Fe1 is the iron site closer to Tyr122, and the two iron sites are high-spin antiferromagnetically coupled to give a total 1/2 net spin), two mu-oxo bridges, one terminal water which binds to Fe1(III) and also H-bonds to both side chains of Asp84 and Glu238, and one bidentate carboxylate group from the side chain of Glu115.
Han
Wen-Ge
WG
Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. wengehan@scripps.edu
Liu
Tiqing
T
Lovell
Timothy
T
Noodleman
Louis
L
D001224:Aspartic Acid / Q000737:chemistry; D001665:Binding Sites; D004578:Electron Spin Resonance Spectroscopy; D018698:Glutamic Acid / Q000737:chemistry; D006860:Hydrogen Bonding; D007501:Iron / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D012262:Ribonucleoside Diphosphate Reductase / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D014867:Water; D001224:Aspartic Acid; D018698:Glutamic Acid; D007501:Iron; D012262:Ribonucleoside Diphosphate Reductase