ArticleJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2011
Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study.
Article in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Lysine or histidine? examining the role of the proximal ligand at the active heme center of cytochrome c nitrite reductase.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2026Article
- Roles of Three Conserved Active Site Residues of CytochromeJournal of the American Chemical Society · 2025Article
- From genes to function: regulation, maturation, and evolution of cytochromeApplied and environmental microbiology · 2025Review
- The Mechanism of Nitrite Reductase.Journal of computational chemistry · 2025Article
- Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2022Review
- Reduction of Substrates by Nitrogenases.Chemical reviews · 2020Review
- The role of porphyrin peripheral substituents in determining the reactivities of ferrous nitrosyl species.Chemical science · 2020Article
- Nitrite and hydroxylamine as nitrogenase substrates: mechanistic implications for the pathway of N₂ reduction.Journal of the American Chemical Society · 2014Article
- Hydrogen bonding networks tune proton-coupled redox steps during the enzymatic six-electron conversion of nitrite to ammonia.Biochemistry · 2014Article
- Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2014Article
- Contrasting catalytic profiles of multiheme nitrite reductases containing CxxCK heme-binding motifs.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2013Article
- Comparative amino acid decomposition analysis of potent type I p38α inhibitors.Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences · 2013Article
- Reductive activation of the heme iron-nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2012Article
- Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2012Article
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2 authors.
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Abstract
Cytochrome c nitrite reductase is a homodimeric enzyme, containing five covalently attached c-type hemes per subunit. Four of the heme irons are bishistidine-ligated, whereas the fifth, the active site of the protein, has an unusual lysine coordination and calcium site nearby. A fascinating feature of this enzyme is that the full six-electron reduction of the nitrite is achieved without release of any detectable reaction intermediate. Moreover, the enzyme is known to work over a wide pH range. Both findings suggest a unique flexibility of the active site in the complicated six-electron, seven-proton reduction process. In the present work, we employed density functional theory to study the energetics and kinetics of the initial stages of nitrite reduction. The possible role of second-sphere active-site amino acids as proton donors was investigated by taking different possible protonation states and geometrical conformations into account. It was found that the most probable proton donor is His(277), whose spatial orientation and fine-tuned acidity lead to energetically feasible, low-barrier protonation reactions. However, substrate protonation may also be accomplished by Arg(114). The calculated barriers for this pathway are only slightly higher than the experimentally determined value of 15.2 kcal/mol for the rate-limiting step. Hence, having proton-donating side chains of different acidity within the active site may increase the operational pH range of the enzyme. Interestingly, Tyr(218), which was proposed to play an important role in the overall mechanism, appears not to take part in the reaction during the initial stage.
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