title: Reductive activation of the heme iron-nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study.
abstract: Cytochrome c nitrite reductase catalyzes the six-electron, seven-proton reduction of nitrite to ammonia without release of any detectable reaction intermediate. This implies a unique flexibility of the active site combined with a finely tuned proton and electron delivery system. In the present work, we employed density functional theory to study the recharging of the active site with protons and electrons through the series of reaction intermediates based on nitrogen monoxide [Fe(II)-NO(+), Fe(II)-NO·, Fe(II)-NO(-), and Fe(II)-HNO]. The activation barriers for the various proton and electron transfer steps were estimated in the framework of Marcus theory. Using the barriers obtained, we simulated the kinetics of the reduction process. We found that the complex recharging process can be accomplished in two possible ways: either through two consecutive proton-coupled electron transfers (PCETs) or in the form of three consecutive elementary steps involving reduction, PCET, and protonation. Kinetic simulations revealed the recharging through two PCETs to be a means of overcoming the predicted deep energetic minimum that is calculated to occur at the stage of the Fe(II)-NO· intermediate. The radical transfer role for the active-site Tyr(218), as proposed in the literature, cannot be confirmed on the basis of our calculations. The role of the highly conserved calcium located in the direct proximity of the active site in proton delivery has also been studied. It was found to play an important role in the substrate conversion through the facilitation of the proton transfer steps.
authors.affiliation: Institut für Physikalische and Theoretische Chemie, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.
authors.forename: Dmytro
authors.initials: D
authors.lastname: Bykov
authors.forename: Frank
authors.initials: F
authors.lastname: Neese
mesh_terms: D020134:Catalytic Domain; D045263:Cytochromes a1 / Q000737:chemistry / Q000378:metabolism*; D003575:Cytochromes c1 / Q000737:chemistry / Q000378:metabolism*; D004579:Electron Transport; D004789:Enzyme Activation; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D007501:Iron / Q000378:metabolism*; D008958:Models, Molecular; D009565:Nitrate Reductases / Q000737:chemistry / Q000378:metabolism*; D009569:Nitric Oxide / Q000378:metabolism*; D009589:Nitrogen Oxides / Q000378:metabolism*; D010084:Oxidation-Reduction; D011522:Protons; D011789:Quantum Theory; D013816:Thermodynamics; D016968:Wolinella / Q000737:chemistry / Q000201:enzymology*
chemical_list: D009589:Nitrogen Oxides; D011522:Protons; D009569:Nitric Oxide; D006418:Heme; C073661:dinitrosyl iron complex; D045263:Cytochromes a1; D003575:Cytochromes c1; D007501:Iron; D009565:Nitrate Reductases; C054690:nitrate reductase (cytochrome)