Pseudospecific docking surfaces on electron transfer proteins as illustrated by pseudoazurin, cytochrome c550 and cytochrome cd1 nitrite reductase

Williams, P.; Fülöp, Vilmos; Leung, Yun-Chung; Chan, Christopher; Moir, James; Howlett, Geoffrey J.; Ferguson, Stuart J.; Radford, Sheena E.; Hajdu, János

doi:10.1038/nsb1195-975

Cited by 117 publications

(118 citation statements)

References 51 publications

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“…The extent of the oxidation of the c heme (and stoichiometric formation of ferrous d 1 heme-NO) varies with enzyme sample up to a maximum of ϳ90%. 5 The conclusion we draw is that on addition of nitrite to reduced enzyme, the substrate binds to the d 1 heme and is rapidly reduced by that heme. This is followed by transfer of the remaining electron on the monomer from the c heme to the heme d 1 -NO complex, with a rate constant of at least 500 s Ϫ1 .…”

Section: Discussionmentioning

confidence: 99%

Time-resolved Infrared Spectroscopy Reveals a Stable Ferric Heme-NO Intermediate in the Reaction of Paracoccus pantotrophus Cytochrome cd 1 Nitrite Reductase with Nitrite

George¹,

Allen²,

Ferguson³

et al. 2000

Journal of Biological Chemistry

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Cytochrome cd 1 is a respiratory enzyme that catalyzes the physiological one-electron reduction of nitrite to nitric oxide. The enzyme is a dimer, each monomer containing one c-type cytochrome center and one active site No kinetically competent release of NO could be detected, indicating that at least one additional factor is required for product release by the enzyme. Implications for the mechanism of P. pantotrophus cytochrome cd 1 are discussed.

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Section: Discussionmentioning

confidence: 99%

Time-resolved Infrared Spectroscopy Reveals a Stable Ferric Heme-NO Intermediate in the Reaction of Paracoccus pantotrophus Cytochrome cd 1 Nitrite Reductase with Nitrite

George¹,

Allen²,

Ferguson³

et al. 2000

Journal of Biological Chemistry

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“…In the surface of the donor protein, besides this region of charged residues, there is a hydrophobic patch that surrounds the exposed entry/exit site of the electron [45]. This hydrophobic patch includes the exposed heme edge in the case of c-type cytochromes or an exposed histidine side chain that coordinates the copper center in the case of pseudoazurins [46,47] (Fig.…”

Section: Resultsmentioning

confidence: 99%

The electron transfer complex between nitrous oxide reductase and its electron donors

Dell’Acqua

Moura

et al. 2011

J Biol Inorg Chem

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Identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. In this study, we focused on the interaction of nitrous oxide reductase (N 2 OR), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. The comparison between the interaction of N 2 OR from three different microorganisms, Pseudomonas nautica, Paracoccus denitrificans, and Achromobacter cycloclastes, with their physiological electron donors was performed through the analysis of the primary sequence alignment, electrostatic surface, and molecular docking simulations, using the bimolecular complex generation with global evaluation and ranking algorithm. The docking results were analyzed taking into account the experimental data, since the interaction is suggested to have either a hydrophobic nature, in the case of P. nautica N 2 OR, or an electrostatic nature, in the case of P. denitrificans N 2 OR and A. cycloclastes N 2 OR. A set of well-conserved residues on the N 2 OR surface were identified as being part of the electron transfer pathway from the redox partner to N 2 OR (Ala495, Asp519, Val524, His566 and Leu568 numbered according to the P. nautica N 2 OR sequence). Moreover, we built a model for Wolinella succinogenes N 2 OR, an enzyme that has an additional c-type-heme-containing domain. The structures of the N 2 OR domain and the c-type-heme-containing domain were modeled and the full-length structure was obtained by molecular docking simulation of these two domains. The orientation of the c-type-heme-containing domain relative to the N 2 OR domain is similar to that found in the other electron transfer complexes.

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“…Thus, the CCP redox partner of cytochrome c550 [23] and its Pseudomonad counterpart [22] are dimers. Pseudoazurin of T. pantotropha, a very close relative of Paracoccus LMD 52.44, is dimeric [24] as is its redox partner nitrite reductase [25]. The families of cytochromes c 5 and c′ are mostly dimeric [26].…”

Section: Discussionmentioning

confidence: 99%

The surface‐charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans @MM implications for the interaction with cytochrome c peroxidase

Pettigrew

Gilmour

Goodhew

et al. 1998

European Journal of Biochemistry

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The implications of the dimeric state of cytochrome c550 for its binding to Paracoccus cytochrome c peroxidase and its delivery of the two electrons required to restore the active enzyme during catalysis have been investigated. The amino acid sequence of cytochrome c550 of Paracoccus denitrificans strain LMD 52.44 was determined and showed 21 differences from that of strain LMD 22.21. Based on the X-ray structure of the latter, a structure for the cytochrome c550 monomer from strain 52.44 is proposed and a dipole moment of 945 debye was calculated with an orientation close to the exposed haem edge. The behaviour of the cytochrome on molecular-exclusion chromatography is indicative of an ionic strength-dependent monomer (15 kDa)/dimer (30 kDa) equilibrium that can also be detected by 1 H-NMR spectroscopy. The apparent mass of 50 kDa observed at very low ionic strength was consistent with the presence of a strongly asymmetric dimer. This was confirmed by cross-linking studies, which showed that a cross-linked species of mass 30 kDa on SDS behaved with an apparent mass of 50 kDa on molecular-exclusion chromatography. A programme which carried out and evaluated molecular docking of two monomers to give a dimer generated a most probable dimer in which the monomer dipoles lay almost antiparallel to each other. The resultant dipole moment of the dimer is therefore small. Although this finding calls into question the possibility of preorientation of a strongly asymmetrically charged cytochrome as it collides with a redox partner, the stoichiometry of complex formation with cytochrome c peroxidase as studied by 1 H-NMR spectroscopy shows that it is the monomer that binds.Keywords : cytochrome; peroxidase ; electron transfer; electrostatic ; dimerisation.Paracoccus denitrificans cytochrome c550 is the electron donor for Paracoccus cytochrome c peroxidase (CCP). We have used these two redox proteins as a model system, with which to investigate and understand electron transfer between proteins. They represent a useful parallel system to the well-studied yeast cytochrome c and yeast CCP [1,2] in that the cytochrome c donors are structurally similar but the peroxidases are quite distinct.Like the yeast peroxidase, the Paracoccus enzyme requires two electrons to restore the active form after oxidation by hydrogen peroxide. In the yeast case, these are probably delivered singly by two ferrocytochrome c molecules sequentially encountering the peroxidase surface. The Paracoccus enzyme contains two haems rather than one, and in separate domains of the protein [3]. One haem is believed to perform an electrontransferring function and the other, a peroxidatic function. With two domains, each carrying an oxidising centre in the intermedi-

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Pseudospecific docking surfaces on electron transfer proteins as illustrated by pseudoazurin, cytochrome c550 and cytochrome cd1 nitrite reductase

Cited by 117 publications

References 51 publications

Time-resolved Infrared Spectroscopy Reveals a Stable Ferric Heme-NO Intermediate in the Reaction of Paracoccus pantotrophus Cytochrome cd 1 Nitrite Reductase with Nitrite

Time-resolved Infrared Spectroscopy Reveals a Stable Ferric Heme-NO Intermediate in the Reaction of Paracoccus pantotrophus Cytochrome cd 1 Nitrite Reductase with Nitrite

The electron transfer complex between nitrous oxide reductase and its electron donors

The surface‐charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans @MM implications for the interaction with cytochrome c peroxidase

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