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PubMed2005

Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase.

The membrane-bound enzyme cytochrome c oxidase is responsible for cell respiration in aerobic organisms and conserves free energy from O2 reduction into an electrochemical proton gradient by coupling the redox reaction to proton-pumping across the membrane. O2 reduction produces water at the bimetallic heme a3/CuB active site next to a hydrophobic cavity deep within the membrane. Water molecules in this cavity have been suggested to play an important role in the proton-pumping mechanism. Here, we show by molecular dynamics simulations that the conserved arginine/heme a3 delta-propionate ion pair provides a gate, which exhibits reversible thermal opening that is governed by the redox state and the water molecules in the cavity. An important role of this gate in the proton-pumping mechanism is supported by site-directed mutagenesis experiments. Transport of the product water out of the enzyme must be rigidly controlled to prevent water-mediated proton leaks that could compromise the proton-pumping function. Exit of product water is observed through the same arginine/propionate gate, which provides an explanation for the observed extraordinary spatial specificity of water expulsion from the enzyme.

Animals↗
PubMed1970

Fluorescent probe environment and the structural and charge changes in energy coupling of mitochondrial membranes.

The use of fluorescent probes to give continuous readouts of the structural states of mitochondrial membranes during energy coupling seems a logical extension of their use in the study of protein structural changes. A clear correlation of the probes' fluorescence characteristics with the acquisition of energy coupling can be demonstrated in fragmented and natural membrane using 1-anilinonaphthalene-8-sulfonate (ANS) and ethidium bromide respectively. The present contribution attempts to bring together contemporary viewpoints of this and other laboratories and the recent experimental data and give some detailed information on probe environment and on the structural or charge changes occurring upon energization. The energy-dependent region of the membrane is located at an aqueous interface between an outer layer of proteins (presumably cytochromes) and the membrane permeability barrier; the aromatic portion of ANS appears to be located in the lipid phase and the sulfonic acid group in the aqueous phase. The aqueous phase is probably a structured water region near paramagnetic membrane components such as cytochrome. Membrane energization arising from altered redox potential changes of cytochromes (b(T)) is communicated to the water structure through altered structural states of the hemoproteins, causing a decreased volume of the structured water region and increased interaction with the paramagnetic components in the energized state. Attendant alterations of protonic equilibria of membrane components induce both local and transmembrane changes in charge distribution, with consequent movements of ions, including the probe molecules themselves.

Animals↗
PubMed1991

Resolution of the electronic transitions of cytochrome c oxidase: evidence for two conformational states of ferrous cytochrome alpha.

Second-derivative absorption spectra are reported for a variety of oxidation and ligation states of bovine cytochrome c oxidase (ferrocytochrome-c:oxygen oxidoreductase, EC 1.9.3.1). The high resolving power of the second-derivative method allows us to assign the individual electronic transitions of cytochrome alpha and cytochrome alpha 3 in many of these states. In the fully reduced enzyme, one observes a single electronic transition at 444 nm, corresponding to the Soret transition for both ferrous cytochrome alpha and ferrous cytochrome alpha 3. When the cytochrome alpha 3 site is occupied by an exogenous ligand (CN or CO), one observes two absorption bands assignable to the ferrous cytochrome alpha chromophore, one at ca, 443 nm and the other at ca, 450 nm. The appearance of the 450-nm band is dependent only on ligand occupancy at the cytochrome alpha 3 site and not on the oxidation state of the cytochrome alpha 3 iron. These results can be interpreted either in terms of a heterogeneous mixture of two ferrous cytochrome alpha conformers in the cytochrome alpha 3-ligated enzyme or in terms of a reduction in the effective molecular symmetry of the ferrous cytochrome alpha site that results in a lifting of the degeneracy of the lowest unoccupied molecular orbital associated with the Soret pi,pi* transition of cytochrome alpha. In either case, the present data indicate that ferrous cytochrome alpha can adopt two distinct conformations. One possible structural difference between these two states could be related to differences in the strength of hydrogen bonding between the ferrous cytochrome alpha formyl oxygen and a proton donor from an unidentified amino acid side chain of the enzyme. The implications of such modulation of hydrogen-bond strength are discussed in terms of possible mechanisms of proton translocation and electron transfer in the enzyme.

Animals↗
PubMed1995

Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.

Amino Acid Sequence↗
PubMed1999

Mass spectrometric determination of dioxygen bond splitting in the "peroxy" intermediate of cytochrome c oxidase.

The "peroxy" intermediate (P form) of bovine cytochrome c oxidase was prepared by reaction of the two-electron reduced mixed-valence CO complex with (18)O(2) after photolytic removal of CO. The water present in the reaction mixture was recovered and analyzed for (18)O enrichment by mass spectrometry. It was found that approximately one oxygen atom ((18)O) per one equivalent of the P form was present in the bulk water. The data show that the oxygen-oxygen dioxygen bond is already broken in the P intermediate and that one oxygen atom can be readily released or exchanged with the oxygen of the solvent water.

Animals↗
PubMed1998

Redox properties of tryptophan tryptophylquinone enzymes. Correlation with structure and reactivity.

The pH dependence of the redox potentials for the oxidized/reduced couples of methylamine dehydrogenase (MADH) and aromatic amine dehydrogenase (AADH) were determined. For each enzyme, a change of -30 mV/pH unit was observed, indicating that the two-electron transfer is linked to the transfer of a single proton. This result differs from what was obtained from redox studies of a tryptophan tryptophylquinone (TTQ) model compound for which the two-electron couple is linked to the transfer of two protons. This result also distinguishes the redox properties of the enzyme-bound TTQ from those of the membrane-bound quinone components of respiratory and photosynthetic electron transfer chains that transfer two protons per two electrons. This difference is attributed to the accessibility of TTQ to solvent in the enzymes. One of the quinol hydroxyls is shielded from solvent and thus is not protonated. The unusual property of TTQ enzymes of stabilizing the anionic form of the reduced quinol is important for the reaction mechanism of MADH because it allows stabilization of physiologically important reaction intermediates. Examination of the extent to which disproportionation of the MADH and AADH semiquinones occurred as a function of pH revealed that the equilibrium concentration of semiquinone increased with pH. This indicates that the proton transfer is linked to the semiquinone/quinol couple. Therefore, the quinol is singly protonated, and the semiquinone is unprotonated and anionic. It was also shown that the oxidation-reduction midpoint potential for AADH is 20 mV less positive than that of MADH over the range of pH values that was studied and that the TTQ semiquinone of AADH was less stable than that of MADH. This may be explained by differences in the active site environments of the two enzymes, which modulate their respective redox properties.

Benzoquinones↗
PubMed2001

Structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase.

Reduction of dioxygen to water is a key process in aerobic life, but atomic details of this reaction have been elusive because of difficulties in observing active oxygen intermediates by crystallography. Cytochrome cd(1) is a bifunctional enzyme, capable of catalyzing the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of dioxygen to water. The latter is a cytochrome oxidase reaction. Here we describe the structure of an active dioxygen species in the enzyme captured by cryo-trapping. The productive binding mode of dioxygen in the active site is very similar to that of nitrite and suggests that the catalytic mechanisms of oxygen reduction and nitrite reduction are closely related. This finding has implications to the understanding of the evolution of oxygen-reducing enzymes. Comparison of the dioxygen complex to complexes of cytochrome cd(1) with stable diatomic ligands shows that nitric oxide and cyanide bind in a similar bent conformation to the iron as dioxygen whereas carbon monoxide forms a linear complex. The significance of these differences is discussed.

Crystallization↗
PubMed2005

Active site aspartate residues are critical for tryptophan tryptophylquinone biogenesis in methylamine dehydrogenase.

The biosynthesis of methylamine dehydrogenase (MADH) requires formation of six intrasubunit disulfide bonds, incorporation of two oxygens into residue betaTrp57 and covalent cross-linking of betaTrp57 to betaTrp108 to form the protein-derived cofactor tryptophan tryptophylquinone (TTQ). Residues betaAsp76 and betaAsp32 are located in close proximity to the quinone oxygens of TTQ in the enzyme active site. These residues are structurally conserved in quinohemoprotein amine dehydrogenase, which possesses a cysteine tryptophylquinone cofactor. Relatively conservative betaD76N and betaD32N mutations resulted in very low levels of MADH expression. Analysis of the isolated proteins by mass spectrometry revealed that each mutation affected TTQ biogenesis. betaD76N MADH possessed the six disulfides but had no oxygen incorporated into betaTrp57 and was completely inactive. The betaD32N MADH preparation contained a major species with six disulfides but no oxygen incorporated into betaTrp57 and a minor species with both oxygens incorporated, which was active. The steady-state kinetic parameters for the betaD32N mutant were significantly altered by the mutation and exhibited a 1000-fold increase in the Km value for methylamine. These results have allowed us to more clearly define the sequence of events that lead to TTQ biogenesis and to define novel roles for aspartate residues in the biogenesis of a protein-derived cofactor.

Aspartic Acid↗
PubMed1978

Irradiation of micro-organisms with mono-energetic X-rays; biological consequences of the Auger effect.

The radiation resonance effect reported previously for isolated biomolecules has now for the first time been observed in a cellular system. Dried bacteria, Micrococcus denitrificans, in which TdR in DNA was partially substituted by BUdR, were subjected to mono-energetic X-rays of energies below or above the K-edge for Br. Subsequently, the colony-forming ability was assayed. For photon energy slightly above the K-edge, the lethality/rad was greater than that below the K-edge. This is interpreted in terms of the Auger effect initiated selectively by photo-absorption in constituent Br atoms. The differential absorption of low-energy photons in constituent atoms of DNA is also discussed.

Animals↗
PubMed1990

Nucleotide sequence of the gene coding for four subunits of cytochrome c oxidase from the thermophilic bacterium PS3.

The gene coding for four subunits of cytochrome aa3-type oxidase was isolated from a genomic DNA library of the thermophilic bacterium PS3 and sequenced. The N-terminus of each subunit was also sequenced to verify the initiation site of the reading frame. The deduced amino acid sequences contained 615 amino acid residues for subunit I (CO1/caaB product), 333 residues for subunit II (CO2/caaA product), 207 residues for subunit III (CO3/caaC product), and 109 residues for subunit IV (CO4/caaD product) after processing. Re-examination of the sequencing of caa revealed a longer open reading frame for CO1, which contains 14 transmembrane segments instead of 12 [Sone et al. (1988) J. Biochem. 103, 606-610], although the main portions of the sequences constituting cytochrome a (FeA), cytochrome a3 (FeB), and CuB are correct. PS3 CO2 has an additional sequence for cytochrome c after the CuA binding protein portion with 2 transmembrane segments, which is homologous to the mitochondrial counterpart. PS3 CO3 has DCCD-binding glutamyl residues but contains only 5 transmembrane segments, unlike the mitochondrial counterpart, which has 7 segments. The subunits of PS3 cytochrome oxidase (aa3-type) show clear similarity in amino acid sequences with those of cytochrome bo-type oxidase from Escherichia coli as well, in spite of the difference of hemes. PS3 CO3 and CO4 are much more similar to E. coli CO3 and CO4 than to mitochondrial CO3 and CO4, respectively.

Amino Acid Sequence↗
PubMed1977

Purification and properties of an acid phosphatase of Micrococcus denitrificans distinct from thiamine phosphate phosphatase.

To determine whether the acid phosphatase in Micrococcus denitrificans participates in hydrolysis of thiamine phosphate in the synthesis of thiamine pyrophosphate, acid phosphatase was purified 280-fold by conventional procedures, which removed thiamine phosphate phosphatase completely. Studies showed that this acid phosphatase is a different protein from thiamine phosphate phosphatase and that it has no binding site for thiamine phosphate on its active site.

Acid Phosphatase↗