X-ray absorption edge determination of the oxidation state and coordination number of copper: application to the type 3 site in Rhus vernicifera laccase and its reaction with oxygen
14 Oct 1987-Journal of the American Chemical Society (American Chemical Society)-Vol. 109, Iss: 21, pp 6433-6442
TL;DR: In this paper, a normalized difference edge analysis is used to quantitatively determine the oxidation states of the copper sites in type 2 copper-depleted (T2D) and native forms of the multicopper oxidase, Rhus vernicifera laccase.
Abstract: Cu X-ray absorption edge features of 19 Cu(I) and 40 Cu(II) model complexes have been systematically studied and correlated with oxidation state and geometry. Studies of Cu(I) model complexes with different coordination number reveal that an 8983-8984-eV peak (assigned as the Cu 1s ..-->.. 4p transition) can be correlated in energy, shape, and intensity with ligation and site geometry of the cuprous ion. These Cu(I) edge features have been qualitatively interpreted with ligand field concepts. Alternatively, no Cu(II) complex exhibits a peak below 8985.0 eV. The limited intensity observed in the 8983-8985-eV region for some Cu(II) complexes is associated with the tail of an absorption peak at approx. 8986 eV which is affected by the covalency of the equatorial ligands. These models studies allow accurate calibration of a normalized difference edge procedure which is used for the quantitative determination of Cu(I) content in copper complexes of mixed oxidation state composition. This normalized difference edge analysis is then used to quantitatively determine the oxidation states of the copper sites in type 2 copper-depleted (T2D) and native forms of the multicopper oxidase, Rhus vernicifera laccase. The type 3 site of the T2D laccase is found to be fully reduced and stable tomore » oxidation by O/sub 2/ or by 25-fold protein equivalents of ferricyanide, but it can be oxidized by reaction with peroxide. The increase in intensity of the 330-nm absorption feature which results from peroxide titration of T2D laccase is found to correlate linearly with the percent of oxidation of the binuclear copper site.« less
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TL;DR: Copper sites have historically been divided into three classes based on their spectroscopic features, which reflect the geometric and electronic structure of the active site: type 1 or blue copper, type 2 (T2) or normal copper, and type 3 (T3) or coupled binuclear copper centers.
Abstract: Copper is an essential trace element in living systems, present in the parts per million concentration range. It is a key cofactor in a diverse array of biological oxidation-reduction reactions. These involve either outer-sphere electron transfer, as in the blue copper proteins and the Cu{sub A} site of cytochrome oxidase and nitrous oxide redutase, or inner-sphere electron transfer in the binding, activation, and reduction of dioxygen, superoxide, nitrite, and nitrous oxide. Copper sites have historically been divided into three classes based on their spectroscopic features, which reflect the geometric and electronic structure of the active site: type 1 (T1) or blue copper, type 2 (T2) or normal copper, and type 3 (T3) or coupled binuclear copper centers. 428 refs.
3,241 citations
TL;DR: In this article, the 1s → 3d pre-edge features of high-spin ferrous and ferric model complexes in octahedral, tetrahedral, and square pyramidal environments were investigated and the allowable many-electron excited states were determined using ligand field theory.
Abstract: X-ray absorption Fe−K edge data on ferrous and ferric model complexes have been studied to establish a detailed understanding of the 1s → 3d pre-edge feature and its sensitivity to the electronic structure of the iron site. The energy position and splitting, and intensity distribution, of the pre-edge feature were found to vary systematically with spin state, oxidation state, geometry, and bridging ligation (for binuclear complexes). A methodology for interpreting the energy splitting and intensity distribution of the 1s → 3d pre-edge features was developed for high-spin ferrous and ferric complexes in octahedral, tetrahedral, and square pyramidal environments and low-spin ferrous and ferric complexes in octahedral environments. In each case, the allowable many-electron excited states were determined using ligand field theory. The energies of the excited states were calculated and compared to the energy splitting in the 1s → 3d pre-edge features. The relative intensities of electric quadrupole transitions...
1,181 citations
TL;DR: This review presents in depth discussions of all these classes of Cu enzymes and the correlations within and among these classes, as well as the present understanding of the enzymology, kinetics, geometric structures, electronic structures and the reaction mechanisms these have elucidated.
Abstract: Based on its generally accessible I/II redox couple and bioavailability, copper plays a wide variety of roles in nature that mostly involve electron transfer (ET), O2 binding, activation and reduction, NO2− and N2O reduction and substrate activation. Copper sites that perform ET are the mononuclear blue Cu site that has a highly covalent CuII-S(Cys) bond and the binuclear CuA site that has a Cu2S(Cys)2 core with a Cu-Cu bond that keeps the site delocalized (Cu(1.5)2) in its oxidized state. In contrast to inorganic Cu complexes, these metalloprotein sites transfer electrons rapidly often over long distances, as has been previously reviewed.1–4 Blue Cu and CuA sites will only be considered here in their relation to intramolecular ET in multi-center enzymes. The focus of this review is on the Cu enzymes (Figure 1). Many are involved in O2 activation and reduction, which has mostly been thought to involve at least two electrons to overcome spin forbiddenness and the low potential of the one electron reduction to superoxide (Figure 2).5,6 Since the Cu(III) redox state has not been observed in biology, this requires either more than one Cu center or one copper and an additional redox active organic cofactor. The latter is formed in a biogenesis reaction of a residue (Tyr) that is also Cu catalyzed in the first turnover of the protein. Recently, however, there have been a number of enzymes suggested to utilize one Cu to activate O2 by 1e− reduction to form a Cu(II)-O2•− intermediate (an innersphere redox process) and it is important to understand the active site requirements to drive this reaction. The oxidases that catalyze the 4e−reduction of O2 to H2O are unique in that they effectively perform this reaction in one step indicating that the free energy barrier for the second two-electron reduction of the peroxide product of the first two-electron step is very low. In nature this requires either a trinuclear Cu cluster (in the multicopper oxidases) or a Cu/Tyr/Heme Fe cluster (in the cytochrome oxidases). The former accomplishes this with almost no overpotential maximizing its ability to oxidize substrates and its utility in biofuel cells, while the latter class of enzymes uses the excess energy to pump protons for ATP synthesis. In bacterial denitrification, a mononuclear Cu center catalyzes the 1e- reduction of nitrite to NO while a unique µ4S2−Cu4 cluster catalyzes the reduction of N2O to N2 and H2O, a 2e− process yet requiring 4Cu’s. Finally there are now several classes of enzymes that utilize an oxidized Cu(II) center to activate a covalently bound substrate to react with O2.
Figure 1
Copper active sites in biology.
Figure 2
Latimer Diagram for Oxygen Reduction at pH = 7.0 Adapted from References 5 and 6.
This review presents in depth discussions of all these classes of Cu enzymes and the correlations within and among these classes. For each class we review our present understanding of the enzymology, kinetics, geometric structures, electronic structures and the reaction mechanisms these have elucidated. While the emphasis here is on the enzymology, model studies have significantly contributed to our understanding of O2 activation by a number of Cu enzymes and are included in appropriate subsections of this review. In general we will consider how the covalency of a Cu(II)–substrate bond can activate the substrate for its spin forbidden reaction with O2, how in binuclear Cu enzymes the exchange coupling between Cu’s overcomes the spin forbiddenness of O2 binding and controls electron transfer to O2 to direct catalysis either to perform two e− electrophilic aromatic substitution or 1e− H-atom abstraction, the type of oxygen intermediate that is required for H-atom abstraction from the strong C-H bond of methane (104 kcal/mol) and how the trinuclear Cu cluster and the Cu/Tyr/Heme Fe cluster achieve their very low barriers for the reductive cleavage of the O-O bond.
Much of the insight available into these mechanisms in Cu biochemistry has come from the application of a wide range of spectroscopies and the correlation of spectroscopic results to electronic structure calculations. Thus we start with a tutorial on the different spectroscopic methods utilized to study mononuclear and multinuclear Cu enzymes and their correlations to different levels of electronic structure calculations.
1,181 citations
1,149 citations
TL;DR: The purpose of this review is to present the information content of spectroscopic methods, which allow one to focus in on the metalloactive site, define its electronic structure, evaluate the role of the protein in determining geometric and Electronic structure, and elucidate the contributions of electronic structure to function.
Abstract: Approximately one-half of all known protein crystal structures in the protein data bank (PDB) contain metal ion cofactors, which play vital roles in charge neutralization, structure, and function.1,2 These proteins range in size from 5000-107 Da with the metal ion corresponding to only on the order of 0.1 wt % of the molecule. Yet, for a wide range of these metalloproteins, the metal ion and its environment are key to the chemistry as these comprise the active site in catalysis. It is the purpose of this review to present the information content of spectroscopic methods, which allow one to focus in on the metalloactive site (Figure 1), define its electronic structure, evaluate the role of the protein in determining geometric and electronic structure, and elucidate the contributions of electronic structure to function. Metalloproteins are simply metal complexes but with remarkably intricate and complex ligands. The metal ion, clusters of metal ions bridged by oxide or sulfide ligands or equatorially chelated by N-heterocyclic ligands (heme, corrin, etc.), are bound to the protein through one or more of the endogenous ligand lone pair donors in Table 1. Note that for most of the donor groups, this requires deprotonation, and the metal ion competition with the proton for the free base lowers the effective pKA by at least several log units from those intrinsic values listed in Table 1. It is important to emphasize that for a number of the ligands in Tables 1 and 2, in particular phenolate, thiolate, oxo and sulfido, and the N-heterocyclic chelates, the metal complex exhibits extremely intense low energy charge transfer (CT) absorption bands, which reflect highly covalent ligand-metal bonds. These make major contributions to the electronic structure of an active site and can be affected by the geometry of the metal site and the orientation of the ligand-metal bond, which in turn can be influenced by the protein matrix. * To whom correspondence should be addressed. † Department of Chemistry, Stanford University. ‡ Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University. 419 Chem. Rev. 2004, 104, 419−458
753 citations