Elucidating the mechanism for the reduction of nitrite by copper nitrite reductase-A contribution from quantum chemical studies

Density functional methods have been applied to investigate the properties of the active site of copper‐containing nitrite reductases and possible reaction mechanisms for the enzyme catalysis. The results for a model of the active site indicate that a hydroxyl intermediate is not formed during the c...

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Bibliographic Details
Published in:Journal of computational chemistry 2007-01, Vol.28 (2), p.528-539
Main Authors: De Marothy, S. A., Blomberg, M. R. A., Siegbahn, P. E. M.
Format: Article
Language:English
Subjects:
Binding Sites
Catalysis
Chemical compounds
Chemical reactions
Computer Simulation
Copper
copper nitrite reductase
Crystallography, X-Ray
density functional theory
Electrons
enzyme mechanisms
Enzymes
Models, Molecular
Molecular Structure
Nitrite Reductases - chemistry
nitrite reduction
Nitrites - chemistry
Oxidation-Reduction
Protons
Quantum Theory
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Summary:Density functional methods have been applied to investigate the properties of the active site of copper‐containing nitrite reductases and possible reaction mechanisms for the enzyme catalysis. The results for a model of the active site indicate that a hydroxyl intermediate is not formed during the catalytic cycle, but rather a state with a protonated nitrite bound to the reduced copper. Electron affinity calculations indicate that reduction of the T2 copper site does not occur immediately after nitrite binding. Proton affinity calculations are indicative of substantial pKa differences between different states of the T2 site. The calculations further suggest that the reaction does not proceed until uptake of a second proton from the bulk solution. They also indicate that Asp‐92 may play both a key role as a proton donor to the substrate, and a structural role in promoting catalysis. In the D92N mutant another base, presumably a nearby histidine (His‐249) may take the role as the proton donor. On the basis of these model calculations and available experimental evidence, an ordered reaction mechanism for the reduction of nitrite is suggested. An investigation of the binding modes of the nitric oxide product and the nitrite substrate to the model site has also been made, indicating that nitric oxide prefers to bind in an end‐on fashion to the reduced T2 site. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 528–539, 2007
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.20567