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Examines the nature and properties of the complex electron-transfer chain formed between flavodoxin and cytochrome c3. Nuclear magnetic resonance protein titrations; Prediction of protein structure by homology modeling; Analysis of the surface electrostatic potentials; Computer graphics modeling of the complex.

The multicopper enzyme nitrous oxide reductase (N2OR) catalyzes the final step of denitrification, the two-electron reduction of N2O to N2. This enzyme is a functional homodimer containing two different multicopper sites: CuA and CuZ. CuA is a binuclear copper site that transfers electrons to the tetranuclear copper sulfide CuZ, the catalytic site. In this study, Pseudomonas nautica cytochrome c552 was identified as the physiological electron donor. The kinetic data show differences when physiological and artificial electron donors are compared [cytochrome vs methylviologen (MV)]. In the presence of cytochrome c552, the reaction rate is dependent on the ET reaction and independent of the N2O concentration. With MV, electron donation is faster than substrate reduction. From the study of cytochrome C552 concentration dependence, we estimate the following kinetic parameters: Kmc552 = 50.2 ± 9.0 4 µM and Vmaxc552 = 1.8 ± 0.6 units/mg. The N2O concentration dependence indicates a KmN2O of 14.0 ± 2.9 µM using MV as the electron donor. The pH effect on the kinetic parameters is different when MV or cytochrome c552 is used as the electron donor (pKa 6.6 or 8.3, respectively). The kinetic study also revealed the hydrophobic nature of the interaction, and direct electron transfer studies showed that CuA is the center that receives electrons from the physiological electron donor. The formation of the electron transfer complex was observed by ¹H NMR protein-protein titrations and was modeled with a molecular docking program (BiGGER). The proposed docked complexes corroborated the ET studies giving a large number of solutions in which cytochrome c552 is placed near a hydrophobic patch located around the CuA center. [ABSTRACT FROM AUTHOR]

The gene for pseudoazurin was isolated from Paracoccus pantotrophus LMD 52.44 and expressed in a heterologous system with a yield of 54.3 mg of pure protein per liter of culture. The gene and protein were shown to be identical to those from P. pantotrophus LMD 82.5. The extinction coefficient of the protein was re-evaluated and was found to be 3.00 mM-1 cm-1 at 590 nm. It was confirmed that the oxidized protein is in a weak monomer/dimer equilibrium that is ionic-strength-dependent. The pseudoazurin was shown to be a highly active electron donor to cytochrome c peroxidase, and activity showed an ionic strength dependence consistent with an electrostatic interaction. The pseudoazurin has a very large dipole moment, the vector of which is positioned at the putative electron-transfer site, His81, and is conserved in this position across a wide range of blue copper proteins. Binding of the peroxidase to pseudoazurin causes perturbation of a set of NMR resonances associated with residues on the His81 face, including a ring of lysine residues. These lysines are associated with acidic residues just back from the rim, the resonances of which are also affected by binding to the peroxidase. We propose that these acidic residues moderate the electrostatic influence of the lysines and so ensure that specific charge interactions do not form across the interface with the peroxidase. [ABSTRACT FROM AUTHOR]

According to the model proposed in previous papers [Pettigrew, G. W., Prazeres, S., Costa, C., Palma, N., Krippahl, L., and Moura, J. J. (1999) The structure of an electron-transfer complex containing a cytochrome c and a peroxidase, J. Biol. Chem. 274, 11383-11389; Pettigrew, G. W., Goodhew, C. F., Cooper, A., Nutley, M., Jumel, K., and Harding, S. E. (2003) Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans, Biochemistry 42, 2046-2055], cytochrome c peroxidase of Paracoccus denitrificans can accommodate horse cytochrome c and Paracoccus cytochrome c[SUB550] at different sites on its molecular surface. Here we use [SUB1]H NMR spectroscopy, analytical ultracentrifugation, molecular docking simulation, and microcalorimetry to investigate whether these small cytochromes can be accommodated simultaneously in the formation of a temary complex. The pattern of perturbation of heme methyl and methionine methyl resonances in binary and ternary solutions shows that a ternary complex can be formed, and this is confirmed by the increase in the sedimentation coefficient upon addition of horse cytochrome c to a solution in which cytochrome c[SUB550] fully occupies its binding site on cytochrome c peroxidase. Docking experiments in which favored binary solutions of cytochrome c[SUB550] bound to cytochrome c peroxidase act as targets for horse cytochrome c and the reciprocal experiments in which favored binary solutions of horse cytochrome c bound to cytochrome c peroxidase act as targets for cytochrome c[SUB550] show that the enzyme can accommodate both cytochromes at the same time on adjacent sites. Microcalorimetric titrations are difficult to interpret but are consistent with a weakened binding of horse cytochrome c to a binary complex of cytochrome c peroxidase and cytochrome c[SUB550] and binding of cytochrome c[SUB550] to the cytochrome c peroxidase that is affected little by the presence of horse cytochrome c in the other site. The presence of a substantial capture surface for small cytochromes on the cytochrome c peroxidase has implications for rate enhancement mechanisms which ensure that the two electrons required for re-reduction of the enzyme after reaction with hydrogen peroxide are delivered efficiently. [ABSTRACT FROM AUTHOR]

Nitrous oxide reductase (N[sub2]OR) catalyzes the two-electron reduction of N[sub2]O to N[sub2] and H[sub2]O in the last step of the bacterial denitrification process. It is a dimeric protein. The recently solved crystal structure of N[sub2]OR indicates that in each subunit there is a Cu[subA] center, which is the electron-transfer site, and a Cu[subZ] center, which is the catalytic site. The neighboring Cu[subA] and Cu[subZ] centers are from different subunits. The whole Cu[subZ] cluster is coordinated by seven His ligands with a weakly bound water at the Cu[subI]/Cu[subIV] edge, which is the substrate access site.