title: Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases.
abstract: Near-IR MCD and variable temperature, variable field (VTVH) MCD have been applied to naphthalene 1,2-dioxygenase (NDO) to describe the coordination geometry and electronic structure of the mononuclear nonheme ferrous catalytic site in the resting and substrate-bound forms with the Rieske 2Fe2S cluster oxidized and reduced. The structural results are correlated with the crystallographic studies of NDO and other related Rieske nonheme iron oxygenases to develop molecular level insights into the structure/function correlation for this class of enzymes. The MCD data for resting NDO with the Rieske center oxidized indicate the presence of a six-coordinate high-spin ferrous site with a weak axial ligand which becomes more tightly coordinated when the Rieske center is reduced. Binding of naphthalene to resting NDO (Rieske oxidized and reduced) converts the six-coordinate sites into five-coordinate (5c) sites with elimination of a water ligand. In the Rieske oxidized form the 5c sites are square pyramidal but transform to a 1:2 mixture of trigonal bipyramial/square pyramidal sites when the Rieske center is reduced. Thus the geometric and electronic structure of the catalytic site in the presence of substrate can be significantly affected by the redox state of the Rieske center. The catalytic ferrous site is primed for the O2 reaction when substrate is bound in the active site in the presence of the reduced Rieske site. These structural changes ensure that two electrons and the substrate are present before the binding and activation of O2, which avoids the uncontrolled formation and release of reactive oxygen species.
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California 94305, USA.
authors.forename: Takehiro
authors.initials: T
authors.lastname: Ohta
authors.forename: Sarmistha
authors.initials: S
authors.lastname: Chakrabarty
authors.forename: John D
authors.initials: JD
authors.lastname: Lipscomb
authors.forename: Edward I
authors.initials: EI
authors.lastname: Solomon
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D049308:Dioxygenases / Q000737:chemistry* / Q000378:metabolism*; D005296:Ferrous Compounds / Q000737:chemistry* / Q000378:metabolism*; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D007211:Indoles / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D009281:Naphthalenes / Q000737:chemistry* / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D011549:Pseudomonas / Q000201:enzymology; D013055:Spectrophotometry, Infrared; D013379:Substrate Specificity
chemical_list: D005296:Ferrous Compounds; D007211:Indoles; D008024:Ligands; D009281:Naphthalenes; C031721:naphthalene; D006418:Heme; C030374:indole; D049308:Dioxygenases