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Tetraazamacrocyclic nickel complexes as models for the active site of methylcoenzyme M reductase
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Journal of Inorganic Biochemistry 96 (2003)
Tetraazamacrocyclic nickel complexes as models for the active site of methylcoenzyme M reductase Mark H Schofield, Williams College, United States David Y Chung, Williams College, United States Methylcoenzyme M reductase, which contains a square planar nickel corphin cofactor, F,,,, catalyzes the final step in methane biosynthesis in methanogenic Archaea. Using chemical reactivity and electrochemical studies as well as spin density (UB3LYP) calculations, several known tetraazamacrocyclic nickel complexes were evaluated for their suitability as chemical mimics for F,,,. Among the candidates studied, only Nickel(II)-7,15-diphenyl-1,5,9,13-tetraazahexadeca1,3,5,7,9,1 I-hexaenato hexafluorophosphate (Ni(II)-[160x]PF,) was found to undergo both reversible oxidation (to Ni(II1)) and quasi-reversible reduction (to Ni(1)). Chemical reduction of Ni-[16ox]PF, by Zn/Hg in DMF affords the Ni(1) (d9) complex confirmed by EPR spectroscopy. Alkylation of Ni(II)-[ 160x]PF, with MeMgBr in THF affords Me-Ni(II)[ 160x] which is dealkylated Hg2+. Ph
Ph
Ph
Ph
Ph
Ph
Crystal structures of reaction intermediates of BphC Toshiva Senda Biological Information Research Center; National Institute of Advanced Industrial Science and Technology, Japan Eiji Masai, Department of BioEngineering, Nagaoka University of Technology, Japan Masao Fukuda, Department of BioEngineering, Nagaoka University of Technology, Japan BphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. Extradiol-cleaving catecholic dioxygenases catalyze the addition of two atomic oxygens to the catechol ring of the substrate, resulting in cleavage of the catechol ring. These enzymes typically contain a non-heme iron (Fe(I1)) in their active site. In order to elucidate the catalytic mechanism of the extradiol-cleaving catecholic dioxygenase, we have tried to solve the crystal structures of reaction intermediates of BphC. Here we present the crystal structures of the substrate free form of BphC, the BphC-substrate (ES) complex, and the BphC-substrate-NO (ES-NO) complex, all of which were determined under anaerobic conditions. These crystal structures revealed the followings. (a) The substrate directly coordinates to the Fe ion as a monoanionic form. (b) Upon substrate binding, His194 makes a conformational change, forming a strong hydrogen bond with hydroxyl group of the substrate. This hydrogen bond seems to be required to deprotonate the hydroxyl group of the substrate. (c) The NO molecule directly coordinates to the Fe ion. The binding site of the NO molecule, which is highly likely to be the binding site of dioxygen, is the vacant site of the octahedral coordination sphere of the ES complex. The cavity that accommodates the NO molecule is lined by hydrophobic residues. On the basisof these findings, we propose a catalytic mechanism of the extraiol-cleaving catecholic dioxygenase in which His194 seemsto play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. Then the protonated His194 seems to stabilize a negative charge on the oxygen molecule located in the hydrophobic oxygen-binding cavity. Finally, protonated His194 seems to function as a proton donor.
Journal of Inorganic Biochemistry 96 (2003)
Tetraazamacrocyclic nickel complexes as models for the active site of methylcoenzyme M reductase Mark H Schofield, Williams College, United States David Y Chung, Williams College, United States Methylcoenzyme M reductase, which contains a square planar nickel corphin cofactor, F,,,, catalyzes the final step in methane biosynthesis in methanogenic Archaea. Using chemical reactivity and electrochemical studies as well as spin density (UB3LYP) calculations, several known tetraazamacrocyclic nickel complexes were evaluated for their suitability as chemical mimics for F,,,. Among the candidates studied, only Nickel(II)-7,15-diphenyl-1,5,9,13-tetraazahexadeca1,3,5,7,9,1 I-hexaenato hexafluorophosphate (Ni(II)-[160x]PF,) was found to undergo both reversible oxidation (to Ni(II1)) and quasi-reversible reduction (to Ni(1)). Chemical reduction of Ni-[16ox]PF, by Zn/Hg in DMF affords the Ni(1) (d9) complex confirmed by EPR spectroscopy. Alkylation of Ni(II)-[ 160x]PF, with MeMgBr in THF affords Me-Ni(II)[ 160x] which is dealkylated Hg2+. Ph
Ph
Ph
Ph
Ph
Ph
Crystal structures of reaction intermediates of BphC Toshiva Senda Biological Information Research Center; National Institute of Advanced Industrial Science and Technology, Japan Eiji Masai, Department of BioEngineering, Nagaoka University of Technology, Japan Masao Fukuda, Department of BioEngineering, Nagaoka University of Technology, Japan BphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. Extradiol-cleaving catecholic dioxygenases catalyze the addition of two atomic oxygens to the catechol ring of the substrate, resulting in cleavage of the catechol ring. These enzymes typically contain a non-heme iron (Fe(I1)) in their active site. In order to elucidate the catalytic mechanism of the extradiol-cleaving catecholic dioxygenase, we have tried to solve the crystal structures of reaction intermediates of BphC. Here we present the crystal structures of the substrate free form of BphC, the BphC-substrate (ES) complex, and the BphC-substrate-NO (ES-NO) complex, all of which were determined under anaerobic conditions. These crystal structures revealed the followings. (a) The substrate directly coordinates to the Fe ion as a monoanionic form. (b) Upon substrate binding, His194 makes a conformational change, forming a strong hydrogen bond with hydroxyl group of the substrate. This hydrogen bond seems to be required to deprotonate the hydroxyl group of the substrate. (c) The NO molecule directly coordinates to the Fe ion. The binding site of the NO molecule, which is highly likely to be the binding site of dioxygen, is the vacant site of the octahedral coordination sphere of the ES complex. The cavity that accommodates the NO molecule is lined by hydrophobic residues. On the basisof these findings, we propose a catalytic mechanism of the extraiol-cleaving catecholic dioxygenase in which His194 seemsto play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. Then the protonated His194 seems to stabilize a negative charge on the oxygen molecule located in the hydrophobic oxygen-binding cavity. Finally, protonated His194 seems to function as a proton donor.