Active site reactant center geometry in the Co(II)-product radical pair state of coenzyme B12-dependent ethanolamine deaminase determined by using orientation-selection electron spin-echo envelope modulation spectroscopy.
The distances and orientations among reactant centers in the active site of coenzyme B12-dependent ethanolamine deaminase from Salmonella typhimurium have been characterized in the Co(II)-product radical pair state by using X-band electron paramagnetic resonance (EPR) and two-pulse electron spin-echo envelope modulation (ESEEM) spectroscopies in the disordered solid state. The unpaired electron spin in the product radical is localized on C2. Our approach is based on the orientation-selection created in the EPR spectrum of the biradical by the axial electron-electron dipolar interaction. Simulation of the EPR line shape yielded a best-fit Co(II)-C2 distance of 9.3 A. ESEEM spectroscopy performed at four magnetic field values addressed the hyperfine coupling of the unpaired electron spin on C2 with 2H in the C5' methyl group of 5'-deoxyadenosine and in the beta-2H position at C1 of the radical. Global ESEEM simulations (over the four magnetic fields) were weighted by the orientation dependence of the EPR line shape. A Nelder-Mead direct search fitting algorithm was used to optimize the simulations. The results lead to a partial model of the active site, in which C5' is located a perpendicular distance of 1.6 A from the Co(II)-C2 axis, at distances of 6.3 and 3.5 A from Co(II) and C2, respectively. The van der Waals contact of the C5'-methyl group and C2 indicates that C5' remains close to the radical species during the rearrangement step. The C2-Hs-C5' angle including the strongly coupled hydrogen, Hs, and the C5'-Hs orientation relative to the C1-C2 axis are consistent with a linear hydrogen atom transfer coordinate and an in-line acceptor p-orbital orientation. The trigonal plane of the C2 atom defines sub-spaces within the active site for C5' radical migration and hydrogen atom transfers (side of the plane facing Co(II)) and amine migration (side of the plane facing away from Co(II)).
Canfield
Jeffrey M
JM
Department of Physics, Emory University, Atlanta, Georgia 30322, USA.
Warncke
Kurt
K
D001665:Binding Sites; D001703:Biophysics / Q000379:methods; D002627:Chemistry, Physical / Q000379:methods; D003035:Cobalt / Q000737:chemistry*; D003038:Cobamides / Q000737:chemistry*; D004574:Electromagnetic Fields; D004578:Electron Spin Resonance Spectroscopy; D004583:Electrons; D004926:Escherichia coli / Q000378:metabolism; D004981:Ethanolamine Ammonia-Lyase / Q000737:chemistry*; D006859:Hydrogen / Q000737:chemistry; D008956:Models, Chemical; D008968:Molecular Conformation; D012486:Salmonella typhimurium / Q000378:metabolism; D013057:Spectrum Analysis
D003038:Cobamides; D003035:Cobalt; D006859:Hydrogen; D004981:Ethanolamine Ammonia-Lyase; C000913:cobamamide