Theoretical study of structure of catalytic copper site in nitrite reductase

Källrot, Niklas; Nilsson, K. Peter R.; Rasmussen, T.; Ryde, Ulf

doi:10.1002/qua.20386

Cited by 24 publications

(46 citation statements)

References 56 publications

(77 reference statements)

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“…This finding is in accordance with theoretical studies on the pH dependence of Cu-NiRs (39). An explicit coupling between structure and activity is emphasized through additional studies showing the reduced nitrite affinity at high pH, by changes in the reduction potential of the type 2 copper ion with pH, and by the presence or absence of protons on the solvent ligands and neighboring residues of the type 2 copper ion.…”

Section: Discussionsupporting

confidence: 88%

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Jacobson

Pistorius

Farkas

et al. 2007

Journal of Biological Chemistry

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Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

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Section: Discussionsupporting

confidence: 88%

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Jacobson

Pistorius

Farkas

et al. 2007

Journal of Biological Chemistry

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“…Unfortunately, it is not physically consistent, but only motivated by the frequent observation that QM/MM methods with electrostatic embedding seem to overestimate electrostatic interactions. 41,49 The ME' method itself, as well as the physically more consistent ME av method, also give better results than QM-only, but with slightly worse MUEs and MSEs than ME scal .…”

Section: Discussionmentioning

confidence: 97%

“…The rationale for this is that it has frequently been observed that electrostatic interaction energies are overestimated by QM/MM. 26,41,42 A problem with all of the previous ME methods is that they are sensitive to the stability of the ESP charges used for the QM system. In particular, for a large QM system, any variation of the charges on the boundary of the QM system will make large contributions to the energy difference between various states, because they are close to the MM system.…”

Section: Mechanical Embeddingmentioning

confidence: 99%

On the Convergence of QM/MM Energies

Söderhjelm

Ryde

2011

J. Chem. Theory Comput.

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198

282

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We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a secondsphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as reference. We have tested 12 different ways to redistribute charges close to the junctions (to avoid overpolarisation of the QM system), but once the junctions are moved away from the active site, there is little need to redistribute the charges. We have tested 13 different variants of QM/MM approaches, including two schemes to correct errors caused by the truncation of the QM system. However, we see little gain from such correction schemes; on the contrary they are sensitive to the charge-redistribution scheme and may cause large errors if charges are close to the junctions. In fact, the best results were obtained with a mechanical embedding approach that does not employ any correction scheme and ignores polarisation. It gives a mean unsigned error for 40 QM systems of different sizes of 7 kJ/mol with a maximum error of 28 kJ/mol. The errors can be significantly decreased if bonds between the QM and MM system (junctions) are moved one residue away from all active-site residues. Then, most QM/MM variants give mean unsigned errors of 5-9 kJ/mol, maximum errors of 16-35 kJ/mol, and only 5-7 residues give an error of over 5 kJ/mol. In general, QM/MM calculations converge faster with system size than pure QM calculations.

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“…[15][16][17] In the following study, the properties of different states of a model CuNiR active site have been investigated through quantum chemical methods, including several possible enzyme mechanism pathways and the geometry of substrate-binding.…”

Section: Introductionmentioning

confidence: 99%

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

2006

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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 pK(a) 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.

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Theoretical study of structure of catalytic copper site in nitrite reductase

Cited by 24 publications

References 56 publications

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

On the Convergence of QM/MM Energies

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

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