Small substrates and cytochrome c are oxidized at different sites of cytochrome c peroxidase

Tuning the peroxidase activity of artificial P450 peroxygenase by engineering redox-sensitive residues

Cytochrome P450 monooxygenases (P450s) are well recognized as versatile bio-oxidation catalysts. However, the catalytic functions of P450s are highly dependent on NAD(P)H and redox partner proteins. Our group has recently reported the use of a dual-functional small molecule (DFSM) for generating peroxygenase activity of P450BM3, a long-chain fatty acid hydroxylase from Bacillus megaterium. The DFSM-facilitated P450BM3 peroxygenase system exhibited excellent peroxygenation activity and regio-/enantioselectivity for various organic substrates, such as styrenes, thioanisole, small alkanes, and alkylbenzenes. Very recently, we demonstrated that the DFSM-facilitated P450BM3 peroxygenase could be switched to a peroxidase by engineering the redox-sensitive tyrosine residues in P450BM3. Given the great potential of P450 peroxidase for C-H oxyfunctionalization, we herein report scrutiny of the effect of mutating redox-sensitive residues on peroxidase activity by deeply screening all redox-sensitive residues of P450BM3, namely methionines, tryptophans, cysteines, and phenylalanines. As a result, six beneficial mutations at positions M212, F81, M112, F173, M177, and F77 were screened out from 78 constructed mutants, and significantly enhanced the peroxidase activity of P450BM3 in the presence of Im-C6-Phe, a typical DFSM molecule. Further combination of the beneficial mutations resulted in a more than 100-fold improvement in peroxidase activity compared with that of the combined parent enzyme and DFSM, comparable to or better than most natural peroxidases. In addition, mutations of redox-sensitive residues even dramatically increased, by more than 300-fold, the peroxidase activity of the starting F87A enzyme in the absence of the DFSM, despite the far lower apparent catalytic turnover number compared with the DFSM-P450 system. This study provides new insights and a potential strategy for regulating the catalytic promiscuity of P450 enzymes for multiple functional oxidations.

Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis

Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.

Ferric heme b in aqueous micellar and vesicular systems: state-of-the-art and challenges

Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the peroxidase activity of HRP as an axial ligand of hemin (proximal His170) and as an acid/base catalyst (distal His42). A key feature of the peroxidase mechanism of HRP is the initial formation of compound I under heterolytic cleavage of added hydrogen peroxide as a terminal oxidant. Investigations of free hemin dispersed in aqueous solution showed that different types of hemin dimers can form, depending on the experimental conditions, possibly resulting in hemin crystallization. Although it has been recognized already in the 1970s that hemin aggregation can be prevented in aqueous solution by using micelle-forming amphiphiles, it remains a challenge to prepare hemin-containing micellar and vesicular systems with peroxidase-like activities. Such systems are of interest as cheap HRP-mimicking catalysts for analytical and synthetic applications. Some of the key concepts on which research in this fascinating and interdisciplinary field is based are summarized, along with major accomplishments and possible directions for further improvement. A systematic analysis of the physico-chemical properties of hemin in aqueous micellar solutions and vesicular dispersions must be combined with a reliable evaluation of its catalytic activity. Future studies should show how well the molecular complexity around hemin in HRP can be mimicked by using micelles or vesicles. Because of the importance of heme b in virtually all biological systems and the fact that porphyrins and hemes can be obtained under potentially prebiotic conditions, ideas exist about the possible role of heme-containing micellar and vesicular systems in prebiotic times.

A Unique P450 Peroxygenase System Facilitated by a Dual-Functional Small Molecule: Concept, Application, and Perspective

Cytochrome P450 monooxygenases (P450s) are promising versatile oxidative biocatalysts. However, the practical use of P450s in vitro is limited by their dependence on the co-enzyme NAD(P)H and the complex electron transport system. Using H₂O₂ simplifies the catalytic cycle of P450s; however, most P450s are inactive in the presence of H₂O₂. By mimicking the molecular structure and catalytic mechanism of natural peroxygenases and peroxidases, an artificial P450 peroxygenase system has been designed with the assistance of a dual-functional small molecule (DFSM). DFSMs, such as N-(ω-imidazolyl fatty acyl)-l-amino acids, use an acyl amino acid as an anchoring group to bind the enzyme, and the imidazolyl group at the other end functions as a general acid-base catalyst in the activation of H₂O₂. In combination with protein engineering, the DFSM-facilitated P450 peroxygenase system has been used in various oxidation reactions of non-native substrates, such as alkene epoxidation, thioanisole sulfoxidation, and alkanes and aromatic hydroxylation, which showed unique activities and selectivity. Moreover, the DFSM-facilitated P450 peroxygenase system can switch to the peroxidase mode by mechanism-guided protein engineering. In this short review, the design, mechanism, evolution, application, and perspective of these novel non-natural P450 peroxygenases for the oxidation of non-native substrates are discussed.

Cytochrome C with peroxidase-like activity encapsulated inside the small DPS protein nanocage

Nature utilizes self-assembled protein-based structures as subcellular compartments in prokaryotes to sequester catalysts for specialized biochemical reactions. These protein cage structures provide unique isolated environments for the encapsulated enzymes. Understanding these systems is useful in the bioinspired design of synthetic catalytic organelle-like nanomaterials. The DNA binding protein from starved cells (Dps), isolated from Sulfolobus solfataricus, is a 9 nm dodecameric protein cage making it the smallest known naturally occurring protein cage. It is naturally over-expressed in response to oxidative stress. The small size, natural biodistribution to the kidney, and ability to cross the glomerular filtration barrier in in vivo experiments highlight its potential as a synthetic antioxidant. Cytochrome C (CytC) is a small heme protein with peroxidase-like activity involved in the electron transport chain and also plays a critical role in cellular apoptosis. Here we report the encapsulation of CytC inside the 5 nm interior cavity of Dps and demonstrate the catalytic activity of the resultant Dps nanocage with enhanced antioxidant behavior. The small cavity can accommodate a single CytC and this was achieved through self-assembly of chimeric cages comprising Dps subunits and a Dps subunit to which the CytC was fused. For selective isolation of CytC containing Dps cages, we utilized engineered polyhistidine tag present only on the enzyme fused Dps subunits (6His-Dps-CytC). The catalytic activity of encapsulated CytC was studied using guaiacol and 3,3',5,5'-tetramethylbenzidine (TMB) as two different peroxidase substrates and compared to the free (unencapsulated) CytC activity. The encapsulated CytC showed better pH dependent catalytic activity compared to free enzyme and provides a proof-of-concept model to engineer these small protein cages for their potential as catalytic nanoreactors.

Purification and Characterization of Two Novel Laccases from Peniophora lycii

Although, currently, more than 100 laccases have been purified from basidiomycete fungi, the majority of these laccases were obtained from fungi of the Polyporales order, and only scarce data are available about the laccases from other fungi. In this article, laccase production by the white-rot basidiomycete fungus Peniophora lycii, belonging to the Russulales order, was investigated. It was shown that, under copper induction, this fungus secreted three different laccase isozymes. Two laccase isozymes—Lac5 and LacA—were purified and their corresponding nucleotide sequences were determined. Both purified laccases were relatively thermostable with periods of half-life at 70 °C of 10 and 8 min for Lac5 and LacA, respectively. The laccases demonstrated the highest activity toward ABTS (97 U·mg⁻¹ for Lac5 and 121 U·mg⁻¹ for LacA at pH 4.5); Lac5 demonstrated the lowest activity toward 2,6-DMP (2.5 U·mg⁻¹ at pH 4.5), while LacA demonstrated this towards gallic acid (1.4 U·mg⁻¹ at pH 4.5). Both Lac5 and LacA were able to efficiently decolorize such dyes as RBBR and Bromcresol Green. Additionally, phylogenetic relationships among laccases of Peniophora spp. were reconstructed, and groups of orthologous genes were determined. Based on these groups, all currently available data about laccases of Peniophora spp. were systematized.

The role of Ala134 in controlling substrate binding and reactivity in ascorbate peroxidase

Ascorbate peroxidase (APX) is a class I heme peroxidase. It has two sites for binding of substrates. One is close to the γ-heme edge and is used for oxidation of ascorbate; the other is at the δ-heme edge and is used for binding of aromatic substrates [Gumiero et al., (2010) Arch. Biochem. Biophys. 500, 13-20]. In this work, we have examined the structural factors that control binding at the δ-heme edge by replacement of Ala134 in APX with a proline residue that is more commonly found in other class II and III peroxidases. Kinetic data indicate that replacement of Ala134 by proline has only a small effect on the catalytic mechanism, or the oxidation of ascorbate or guaiacol. Chemical modification with phenylhydrazine indicates that heme accessibility close to the δ-heme edge is only minorly affected by the substitution. We conclude that the A134P mutation alone is not enough to substantially affect the reactivity of APX towards aromatic substrates bound at the δ-heme edge. The data are relevant to the recent application of APX (APEX) in cellular imaging.

Use of apomyoglobin to gently remove heme from a H2O2-dependent cytochrome P450 and allow its reconstitution

Apo-P450 can be prepared under mild conditions using apo-myoglobin as a heme scavenger and it can be reconstituted with hemin or manganese protoporphyrin IX.

Structural basis for cytochrome c Y67H mutant to function as a peroxidase

The catalytic activity of cytochrome c (cyt c) to peroxidize cardiolipin to its oxidized form is required for the release of pro-apoptotic factors from mitochondria, and for execution of the subsequent apoptotic steps. However, the structural basis for this peroxidation reaction remains unclear. In this paper, we determined the three-dimensional NMR solution structure of yeast cyt c Y67H variant with high peroxidase activity, which is almost similar to that of its native form. The structure reveals that the hydrogen bond between Met80 and residue 67 is disrupted. This change destabilizes the sixth coordination bond between heme Fe³⁺ ion and Met80 sulfur atom in the Y67H variant, and further makes it more easily be broken at low pH conditions. The steady-state studies indicate that the Y67H variant has the highest peroxidase activities when pH condition is between 4.0 and 5.2. Finally, a mechanism is suggested for the peroxidation of cardiolipin catalyzed by the Y67H variant, where the residue His67 acts as a distal histidine, its protonation facilitates O-O bond cleavage of H₂O₂ by functioning as an acidic catalyst.

Regulatory Fe(II/III) heme: the reconstruction of a molecule's biography

More than 20 years of research on heme as a temporary effector molecule of proteins have revealed its widespread impact on virtually all primary functions in the human organism. As our understanding of this influence is still growing, a comprehensive overview of compiled data will give fresh impetus for creativity and developing new strategies in heme-related research. From known data concerning heme-regulated proteins and their involvement in the development of diseases, we provide concise information of Fe(II/III) heme as a regulator and the availability of "regulatory heme". The latter is dependent on the balance between free and bound Fe(II/III) heme, here termed "hemeostasis". Imbalance of this system can lead to the development of diseases that were not always attributed to this small molecule. Diseases such as cancer or Alzheimer's disease highlight the reawakened interest in heme, whose function was previously believed to be completely understood.

Structure of a mitochondrial cytochrome c conformer competent for peroxidase activity

At the onset of apoptosis, the peroxidation of cardiolipin at the inner mitochondrial membrane by cytochrome c requires an open coordination site on the heme. We report a 1.45-Å resolution structure of yeast iso-1-cytochrome c with the Met80 heme ligand swung out of the heme crevice and replaced by a water molecule. This conformational change requires modest adjustments to the main chain of the heme crevice loop and is facilitated by a trimethyllysine 72-to-alanine mutation. This mutation also enhances the peroxidase activity of iso-1-cytochrome c. The structure shows a buried water channel capable of facilitating peroxide access to the active site and of moving protons produced during peroxidase activity to the protein surface. Alternate positions of the side chain of Arg38 appear to mediate opening and closing of the buried water channel. In addition, two buried water molecules can adopt alternate positions that change the network of hydrogen bonds in the buried water channel. Taken together, these observations suggest that low and high proton conductivity states may mediate peroxidase function. Comparison of yeast and mammalian cytochrome c sequences, in the context of the steric factors that permit opening of the heme crevice, suggests that higher organisms have evolved to inhibit peroxidase activity, providing a more stringent barrier to the onset of apoptosis.

Enhancement of enzymatic activity for myoglobins by modification of heme-propionate side chains

The modification of myoglobin is an attractive process not only for understanding its molecular mechanism but also for engineering the protein function. The strategy of myoglobin functionalization can be divided into at least two approaches: site-directed mutagenesis and reconstitution with a non-natural prosthetic group. The former method enables us to mainly modulate the physiological function, while the latter has the advantage of introducing a new function on the protein. Particularly, replacement of the native hemin with an artificially created hemin having hydrophobic moieties at the terminal of the heme-propionate side chains serves as an appropriate substrate-binding site near the heme pocket, and consequently enhances the peroxidase and peroxygenase activities for the reconstituted myoglobin. In addition, the incorporation of the synthetic hemin bearing modified heme-propionates into an appropriate apomyoglobin mutant drastically enhances the peroxidase activity. In contrast, to convert myoglobin into a cytochrome P450 enzyme, a flavin moiety as an electron transfer mediator was introduced at the terminal of the heme-propionate side chain. The flavomyoglobin catalyzes the deformylation of 2-phenylpropanal in the presence of NADH under aerobic conditions through the peroxoanion formation from the oxygenated species. In addition, modification of the heme-propionate side chains has an significant influence on regulating the reactivity of the horseradish peroxidase. Furthermore, the heme-propionate side chain can form a metal binding site with a carboxylate residue in the heme pocket. These studies indicate that modification of the heme-propionate side chains can be a new and effective way to engineer functions for the hemoproteins.

Crystal structure of guaiacol and phenol bound to a heme peroxidase

Guaiacol is a universal substrate for all peroxidases, and its use in a simple colorimetric assay has wide applications. However, its exact binding location has never been defined. Here we report the crystal structures of guaiacol bound to cytochrome c peroxidase (CcP). A related structure with phenol bound is also presented. The CcP-guaiacol and CcP-phenol crystal structures show that both guaiacol and phenol bind at sites distinct from the cytochrome c binding site and from the δ-heme edge, which is known to be the binding site for other substrates. Although neither guaiacol nor phenol is seen bound at the δ-heme edge in the crystal structures, inhibition data and mutagenesis strongly suggest that the catalytic binding site for aromatic compounds is the δ-heme edge in CcP. The functional implications of these observations are discussed in terms of our existing understanding of substrate binding in peroxidases [Gumiero A et al. (2010) Arch Biochem Biophys 500, 13-20].

Role of proximal methionine residues in Leishmania major peroxidase

The active site architecture of Leishmania major peroxidase (LmP) is very similar with both cytochrome c peroxidase and ascorbate peroxidase. We utilized point mutagenesis to investigate if the conserved proximal methionine residues (Met248 and Met249) in LmP help in controlling catalysis. Steady-state kinetics of methionine mutants shows that ferrocytochrome c oxidation is <2% of wild type levels without affecting the second order rate constant of first phase of Compound I formation, while the activity toward a small molecule substrate, guaiacol or iodide, increases. Our diode array stopped-flow spectral studies show that the porphyrin π-cation radical of Compound I in mutant LmP is more stable than wild type enzyme. These results suggest that the electronegative sulfur atoms of the proximal pocket are critical factors for controlling the location of a stable Compound I radical in heme peroxidases and are important in the oxidation of ferrocytochrome c.

Peroxidase activity enhancement of horse cytochrome c by dimerization

The peroxidase activity of horse cytochrome c was enhanced by its dimerization, where its Compound III (oxy-form) and Compound I (oxoferryl porphyrin π-cation radical) species were detected in the reactions with hydrogen peroxide and meta-chloroperbenzoic acid, respectively. These results show that oligomeric cytochrome c can contribute as a proapoptotic conformer by the increased peroxidase activity.

Thirty years of heme peroxidase structural biology

The following is a brief review of peroxidase structural biology since the initial structure determination of cytochrome c peroxidase (CCP) 30 years ago. An emphasis will be placed on what CCP has taught us about peroxidase mechanisms, especially Compound I formation and electron transfer.

Crystal structure and peroxidase activity of myoglobin reconstituted with iron porphycene

The incorporation of an artificially created metal complex into an apomyoglobin is one of the attractive methods in a series of hemoprotein modifications. Single crystals of sperm whale myoglobin reconstituted with 13,16-dicarboxyethyl-2,7-diethyl-3,6,12,17-tetramethylporphycenatoiron(III) were obtained in the imidazole buffer, and the 3D structure with a 2.25-A resolution indicates that the iron porphycene, a structural isomer of hemin, is located in the normal position of the heme pocket. Furthermore, it was found that the reconstituted myoglobin catalyzed the H2O2-dependent oxidations of substrates such as guaiacol, thioanisole, and styrene. At pH 7.0 and 20 degrees C, the initial rate of the guaiacol oxidation is 11-fold faster than that observed for the native myoglobin. Moreover, the stopped-flow analysis of the reaction of the reconstituted protein with H2O2 suggested the formation of two reaction intermediates, compounds II- and III-like species, in the absence of a substrate. It is a rare example that compound III is formed via compound II in myoglobin chemistry. The enhancement of the peroxidase activity and the formation of the stable compound III in myoglobin with iron porphycene mainly arise from the strong coordination of the Fe-His93 bond.

Crystal structure of the ascorbate peroxidase-salicylhydroxamic acid complex

Ascorbate peroxidase is a bifunctional peroxidase that catalyzes the H(2)O(2)-dependent oxidation of both ascorbate and various aromatic substrates. The ascorbate binding site was recently identified as being close to the gamma-heme edge [Sharp, K. H., Mewies, M., Moody, P. C. E., and Raven, E. L. (2003)Nat. Struct. Biol. 10, 303-307]. In this work, the X-ray crystal structure of recombinant soybean cytosolic ascorbate peroxidase (rsAPX) in complex with salicylhydroxamic acid (SHA) has been determined to 1.46 A. The SHA molecule is bound close to the delta-heme edge in a cavity that connects the distal side of the heme to the surface of the protein. There are hydrogen bonds between the phenolic hydroxide of the SHA and the main chain carbonyl of Pro132, between the carbonyl oxygen of SHA and the side chain guanadinium group of Arg38, and between the hydroxamic acid group and the indole nitrogen of Trp41. The structure provides the first information about the location of the aromatic binding site in ascorbate peroxidase and, together with our previous data [Sharp, K. H., et al. (2003) Nat. Struct. Biol. 10, 303-307], completes the structural description of the binding properties of ascorbate peroxidase. The mechanistic implications of the results are discussed in terms of our current understanding of how APX catalyzes oxidation of different types of substrates bound at different locations.

Hybridization of Modified-Heme Reconstitution and Distal Histidine Mutation to Functionalize Sperm Whale Myoglobin

To modulate the physiological function of a hemoprotein, most approaches have been demonstrated by site-directed mutagenesis. Replacement of the native heme with an artificial prosthetic group is another way to modify a hemoprotein. However, an alternate method, mutation or heme reconstitution, does not always demonstrate sufficient improvement compared with the native heme enzyme. In the present study, to convert a simple oxygen storage hemoprotein, myoglobin, into an active peroxidase, we applied both methods at the same time. The native heme of myoglobin was replaced with a chemically modified heme 2 having two aromatic rings at the heme-propionate termini. The constructed myoglobins were examined for 2-methoxyphenol (guaiacol) oxidation in the presence of H2O2. Compared with native myoglobin, rMb(H64D.2) showed a 430-fold higher kcat/Km value, which is significantly higher than that of cytochrome c peroxidase and only 3-fold less than that of horseradish peroxidase. In addition, myoglobin-catalyzed degradation of bisphenol A was examined by HPLC analysis. The rMb(H64D.2) showed drastic acceleration (>35-fold) of bisphenol A degradation compared with the native myoglobin. In this system, a highly oxidized heme reactive species is smoothly generated and a substrate is effectively bound in the heme pocket, while native myoglobin only reversibly binds dioxygen. The present results indicate that the combination of a modified-heme reconstitution and an amino acid mutation should offer interesting perspectives toward developing a useful biomolecule catalyst from a hemoprotein.

Substrate binding and catalytic mechanism in ascorbate peroxidase: evidence for two ascorbate binding sites

The catalytic mechanism of recombinant soybean cytosolic ascorbate peroxidase (rsAPX) and a derivative of rsAPX in which a cysteine residue (Cys32) located close to the substrate (L-ascorbic acid) binding site has been modified to preclude binding of ascorbate [Mandelman, D., Jamal, J., and Poulos, T. L. (1998) Biochemistry 37, 17610-17617] has been examined using pre-steady-state and steady-state kinetic techniques. Formation (k1 = 3.3 +/- 0.1 x 10(7) M(-1) s(-1)) of Compound I and reduction (k(2) = 5.2 +/- 0.3 x 10(6) M(-1) s(-1)) of Compound I by substrate are fast. Wavelength maxima for Compound I of rsAPX (lambda(max) (nm) = 409, 530, 569, 655) are consistent with a porphyrin pi-cation radical. Reduction of Compound II by L-ascorbate is rate-limiting: at low substrate concentration (0-500 microM), kinetic traces were monophasic but above approximately 500 microM were biphasic. Observed rate constants for the fast phase overlaid with observed rate constants extracted from the (monophasic) dependence observed below 500 microM and showed saturation kinetics; rate constants for the slow phase were linearly dependent on substrate concentration (k(3-slow)) = 3.1 +/- 0.1 x 10(3) M(-1) s(-1)). Kinetic transients for reduction of Compound II by L-ascorbic acid for Cys32-modified rsAPX are monophasic at all substrate concentrations, and the second-order rate constant (k(3) = 0.9 +/- 0.1 x 10(3) M(-1) s(-1)) is similar to that obtained from the slow phase of Compound II reduction for unmodified rsAPX. Steady-state oxidation of L-ascorbate by rsAPX showed a sigmoidal dependence on substrate concentration and data were satisfactorily rationalized using the Hill equation; oxidation of L-ascorbic acid by Cys32-modified rsAPX showed no evidence of sigmoidal behavior. The data are consistent with the presence of two kinetically competent binding sites for ascorbate in APX.

Mesopone cytochrome c peroxidase: functional model of heme oxygenated oxidases

The effect of heme ring oxygenation on enzyme structure and function has been examined in a reconstituted cytochrome c peroxidase. Oxochlorin derivatives were formed by OsO(4) treatment of mesoporphyrin followed by acid-catalyzed pinacol rearrangement. The northern oxochlorin isomers were isolated by chromatography, and the regio-isomers assignments determined by 2D COSY and NOE 1H NMR. The major isomer, 4-mesoporphyrinone (Mp), was metallated with FeCl(2) and reconstituted into cytochrome c peroxidase (CcP) forming a hybrid green protein, MpCcP. The heme-altered enzyme has 99% wild-type peroxidase activity with cytochrome c. EPR spectroscopy of MpCcP intermediate compound I verifies the formation of the Trp(191) radical similar to wild-type CcP in the reaction cycle. Peroxidase activity with small molecules is varied: guaiacol turnover increases approximately five-fold while that with ferrocyanide is approximately 85% of native. The electron-withdrawing oxo-substitutents on the cofactor cause a approximately 60-mV increase in Fe(III)/Fe(II) reduction potential. The present investigation represents the first structural characterization of an oxochlorin protein with X-ray intensity data collected to 1.70 A. Although a mixture of R- and S-mesopone isomers of the FeMP cofactor was used during heme incorporation into the apo-protein, only the S-isomer is found in the crystallized protein.

Role of the low-affinity binding site in electron transfer from cytochrome C to cytochrome C peroxidase

The interaction of yeast iso-1-cytochrome c (yCc) with the high- and low-affinity binding sites on cytochrome c peroxidase compound I (CMPI) was studied by stopped-flow spectroscopy. When 3 microM reduced yCc(II) was mixed with 0.5 microM CMPI at 10 mM ionic strength, the Trp-191 radical cation was reduced from the high-affinity site with an apparent rate constant >3000 s(-1), followed by slow reduction of the oxyferryl heme with a rate constant of only 10 s(-1). In contrast, mixing 3 microM reduced yCc(II) with 0.5 microM preformed CMPI *yCc(III) complex led to reduction of the radical cation with a rate constant of 10 s(-1), followed by reduction of the oxyferryl heme in compound II with the same rate constant. The rate constants for reduction of the radical cation and the oxyferryl heme both increased with increasing concentrations of yCc(II) and remained equal to each other. These results are consistent with a mechanism in which both the Trp-191 radical cation and the oxyferryl heme are reduced by yCc(II) in the high-affinity binding site, and the reaction is rate-limited by product dissociation of yCc(III) from the high-affinity site with apparent rate constant k(d). Binding yCc(II) to the low-affinity site is proposed to increase the rate constant for dissociation of yCc(III) from the high-affinity site in a substrate-assisted product dissociation mechanism. The value of k(d) is <5 s(-1) for the 1:1 complex and >2000 s(-1) for the 2:1 complex at 10 mM ionic strength. The reaction of horse Cc(II) with CMPI was greatly inhibited by binding 1 equiv of yCc(III) to the high-affinity site, providing evidence that reduction of the oxyferryl heme involves electron transfer from the high-affinity binding site rather than the low-affinity site. The effects of CcP surface mutations on the dissociation rate constant indicate that the high-affinity binding site used for the reaction in solution is the same as the one identified in the yCc*CcP crystal structure.

Cation-induced stabilization of the engineered cation-binding loop in cytochrome c peroxidase (CcP)

We have previously shown that the K(+) site found in the proximal heme pocket of ascorbate peroxidase (APX) could be successfully engineered into the closely homologous cytochrome c peroxidase (CcP) [Bonagura et al., (1996) Biochemistry 35, 6107-6115; Bonagura et al. (1999) Biochemistry 38, 5538-5545]. In addition, specificity could be switched to binding Ca(2+) as found in other peroxidases [Bonagura et al. (1999) J. Biol. Chem. 274, 37827-37833]. The introduction of a proximal cation-binding site also promotes conversion of the Trp191 containing cation-binding loop from a "closed" to an "open" conformer. In the present study we have changed a crucial hinge residue of the cation-binding loop, Asn195, to Pro which stabilizes the loop, albeit, only in the presence of bound K(+). The crystal structure of this mutant, N195PK2, has been refined to 1.9 A. As predicted, introduction of this crucial hinge residue stabilizes the cation-binding loop in the presence of the bound K(+). As in earlier work, the characteristic EPR signal of Trp191 cation radical becomes progressively weaker with increasing [K(+)] and the lifetime of the Trp191 radical also has been considerably shortened in this mutant. This mutant CcP exhibits reduced enzyme activity, which could be titrated to lower levels with increasing [K(+)] when horse heart cytochrome c is the substrate. However, with yeast cytochrome c as the substrate, the mutant was as active as wild-type at low ionic strength, but 40-fold lower at high ionic strength. We attribute this difference to a change in the rate-limiting step as a function of ionic strength when yeast cytochrome c is the substrate.

Changing the substrate specificity of cytochrome c peroxidase using directed evolution

Cytochrome c peroxidase (CCP) from Saccharomyces cerevisiae was subjected to directed molecular evolution to generate mutants with increased activity against 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). Using a combination of DNA shuffling and saturation mutagenesis, mutants were isolated which possessed more than 20-fold increased activity against ABTS and a 70-fold increased specificity toward ABTS compared to the natural substrate. In contrast, activities against another small organic molecule, guaiacol, were not significantly affected. Mutations at residues Asp224 and Asp217 were responsible for this increase in activity. These two residues are located on the surface of the protein and not in the direct vicinity of the distal cavity of the peroxidase, where small organic substrates are believed to be oxidized. Mutations at position Asp224 also lead to an increased amount of the active holoenzyme expressed in Escherichia coli, favoring the selection of these mutants in the employed colony screen. Possible explanations for the effect of the mutations on the in vitro activity of CCP as well as the increased amount of holoenzyme are discussed.

Kinetic differences of purified laccases from six Pleurotus ostreatus strains

AIMS

Enzyme kinetics of purified laccases from six different Pleurotus ostreatus strains were determined in the oxidation of syringaldazine, guaiacol and ABTS.

METHODS AND RESULTS

Significant differences in the kinetic constants were found. Catalytic activity (kcat) ranged from 19 to 941 U mg(-1) for syringaldazine, from 18 to 1565 U mg(-1) for ABTS, and from 4 to 44 U mg(-1) for guaiacol. The apparent affinity constants (KM) also showed significant differences between the different strains, from 12 to 52 micromol l(-1) for syringaldazine, from 8 to 79 micromol l(-1) for ABTS, and from 0.46 to 6.61 mmol l(-1) for guaiacol. No differences were found either on the effect of increasing concentrations of organic solvent (acetonitrile) or on the activity pH profile. The temperature profile was the same for all the P. ostreatus strains, except for the IE8 strain, which seems to be more sensitive to temperature. The kinetic and stability data from the six P. ostreatus strains were also compared with those obtained from other white rot fungi, Coriolopsis gallica and Trametes versicolor, showing clear differences.

CONCLUSION

The different P. ostreatus isolates showed different kinetic constants.

SIGNIFICANCE AND IMPACT OF THE STUDY

The different enzymatic properties of laccases from various P. ostreatus strains should be considered for a potential industrial or environmental application.

Peroxidase-catalyzed oxidation of ascorbate. Structural, spectroscopic and mechanistic correlations in ascorbate peroxidase

Ascorbate-dependent peroxidase activity was first reported in 1979 (Groden and Beck, 1979; Kelly and Latzko, 1979) and ascorbate peroxidase (APX) is, therefore, a relative newcomer to the peroxidase field--horseradish (HRP) and cytochrome c (CcP) peroxidases were, for example, first identified in 1903 (Bach and Chodat, 1903) and 1940 (Altschul et al., 1940) respectively. The APX area was reviewed by Dalton in 1991 (Dalton, 1991): at that time, there was very little detailed kinetic, spectroscopic or functional information available and no structural information had been published. Since 1991, there have been some major advances in the field, most notably with the publication, in 1995, of the first crystal structure for an APX enzyme (Patterson and Poulos, 1995). This information, together with the availability of new recombinant expression systems (Yoshimura et al., 1998; Caldwell et al., 1998; Dalton et al., 1996; Patterson and Poulos, 1994), served as a catalyst for the publication of new functional and spectroscopic data and has meant these data could be sensibly rationalized at the molecular level. The aim of this review is to summarize the more recent advances in the APX area and, as far as possible, to draw comparisons with other, more well-characterized peroxidases. The review will concentrate on the ways in which structural, spectroscopic and mechanistic information have been used in a complementary way to provide a more detailed picture of APX catalysis. The more biological and physiological aspects of APX enzymes have been previously covered in a comprehensive manner (Dalton, 1991) and will not, therefore, be dealt with in detail here.

Directed molecular evolution of cytochrome c peroxidase

Cytochrome c peroxidase (CCP) from Saccharomyces cerevisiae was subjected to directed molecular evolution to generate mutants with increased activity against the classical peroxidase substrate guaiacol, thus changing the substrate specificity of CCP from the protein cytochrome c to a small organic molecule. After three rounds of DNA shuffling and screening, mutants were isolated which possessed a 300-fold increased activity against guaiacol and an up to 1000-fold increased specificity for this substrate relative to that for the natural substrate. In all of the selected mutants, the distal arginine (Arg48), which is fully conserved in the superfamily of peroxidases, was mutated to histidine, showing that this mutation plays a key role in the significant increase in activity against phenolic substrates. The results suggest that, in addition to stabilizing the reactive intermediate compound I, the distal arginine plays an important role as a gatekeeper in the active site of CCP, controlling the access to the ferryl oxygen and the distal histidine. Other isolated mutations increase the general reactivity of the peroxidase or increase the intracellular concentration of the active holo form, allowing their selection under the employed screening conditions. The results illustrate the ability of directed molecular evolution technologies to deliver solutions to biochemical problems that would not be readily predicted by rational design.

The effects of an engineered cation site on the structure, activity, and EPR properties of cytochrome c peroxidase

Earlier work [Bonagura et al. (1996) Biochemistry 35, 6107] showed that the K+ site found in the proximal pocket of ascorbate peroxidase (APX) could be engineered into cytochrome c peroxidase (CCP). Binding of K+ at the engineered site results in a loss in activity and destabilization of the CCP compound I Trp191 cationic radical owing to long-range electrostatic effects. The engineered CCP mutant crystal structure has been refined to 1.5 A using data obtained at cryogenic temperatures which provides a more detailed basis for comparison with the naturally occurring K+ site in APX. The characteristic EPR signal associated with the Trp191 radical becomes progressively weaker as K+ is added, which correlates well with the loss in enzyme activity as [K+] is increased. These results coupled with stopped-flow studies support our earlier conclusions that the loss in activity and EPR signal is due to destabilization of the Trp191 cationic radical.

Redox activity of tryptophan residues in recombinant cytochrome c peroxidase and its W51F and W191F mutants

Tryptophan oxidation mediated via the heme was initiated by adding 2, 6, and 20 equivalents of H2O2to 5 μM recombinant CCP (CCP(MI)) and its W51F and W19lF mutants at pH 7.0. Addition of the proteins to 8 M urea (pH 1.5) relieved heme quenching of Trp fluorescence. CCP(MI)-I, W51F-I, and W19lF-I, the two-electron oxidized species (Fe1V=O,R•+) formed on addition of 2 equivalents of H2O2, exhibited decreased fluorescence relative to the FeIIIforms. Loss of 0.7 Trp in CCP(MI)-I and W51F-I, and 0.2 Trp in W19lF-I implies that R•+is located on Trp19l in CCP(MI)-I and W51F-I Spontaneous decay of the Fe1V=O hemes back to FeIII, followed by reaction with 2 more equivalents of H2O2after 24 h, resulted in a combined loss of 2.7 (CCP(MI)), 1.5 (W51F), and ~1 (W19lF) Trp. Also, addition of 6 equivalents of H2O2to the resting FeIIIenzymes resulted in loss of ~2 Trps in CCP(MI) but only ~1 in W51F and W19lF, suggesting that Trp51 becomes redox active in CCP(MI) when > 2 equivalents of H2O2are reduced. Addition of 20 equivalents of H2O2resulted in a total loss of ~4,2.5, and 2 Trp in CCP(MI), W51F, and W19lF, respectively. Activity loss largely paralleled Trp loss, and the residual activity of CCP(MI) and W51F exposed to 20 equivalents of H2O2was 5–19%, while W19lF exhibited ~50% activity. SDS PAGE analysis revealed that oxidized CCP(MI) and W19lF were 60–70% monomeric, and W51F 27% monomeric following its reaction with > 2 equivalents H2O2. Amino acid analyses confirmed Trp loss and also showed significant Tyr, but not Met, loss in the oxidized proteins. Donors to the heme and pathways of electron migration are proposed based on the combined results. Key words: cytochrome c peroxidase, Trp mutants, H2O2oxidation, redox-active residues.

An engineered cation site in cytochrome c peroxidase alters the reactivity of the redox active tryptophan

The crystal structures of cytochrome c peroxidase and ascorbate peroxidase are very similar, including the active site architecture. Both peroxidases have a tryptophan residue, designated the proximal Trp, located directly adjacent to the proximal histidine heme ligand. During the catalytic cycle, the proximal Trp in cytochrome c peroxidase is oxidized to a cation radical. However, in ascorbate peroxidase, the porphyrin is oxidized, not the proximal Trp, despite the close similarity between the two peroxidase active site structures. A cation located approximately 8 A from the proximal Trp in ascorbate peroxidase but absent in cytochrome c peroxidase is thought to be one reason why ascorbate peroxidase does not form a Trp radical. Site-directed mutagenesis has been used to introduce the ascorbate peroxidase cation binding site into cytochrome c peroxidase. Crystal structures show that mutants now bind a cation. Electron paramagnetic resonance spectroscopy shows that the cation-containing mutants of cytochrome c peroxidase no longer form a stable Trp radical. The activity of the cation mutants using ferrocytochrome c as a substrate is < 1% of wild type levels, while the activity toward a small molecule substrate, guaiacol, increases. These results demonstrate that long range electrostatic effects can control the reactivity of a redox active amino acid side chain and that oxidation/reduction of the proximal Trp is important in the oxidation of ferrocytochrome c.

Altering substrate specificity at the heme edge of cytochrome c peroxidase

Two mutants of cytochrome c peroxidase (CCP) are reported which exhibit unique specificities toward oxidation of small substrates. Ala-147 in CCP is located near the delta-meso edge of the heme and along the solvent access channel through which H2O2 is thought to approach the active site. This residue was replaced with Met and Tyr to investigate the hypothesis that small molecule substrates are oxidized at the exposed delta-meso edge of the heme. X-ray crystallographic analyses confirm that the side chains of A147M and A147Y are positioned over the delta-meso heme position and might therefore modify small molecule access to the oxidized heme cofactor. Steady-state kinetic measurements show that cytochrome c oxidation is enhanced 3-fold for A147Y relative to wild type, while small molecule oxidation is altered to varying degrees depending on the substrate and mutant. For example, oxidation of phenols by A147Y is reduced to less than 20% relative to the wild-type enzyme, while Vmax/e for oxidation of other small molecules is less affected by either mutation. However, the "specificity" of aniline oxidation by A147M, i.e., (Vmax/e)/Km, is 43-fold higher than in wild-type enzyme, suggesting that a specific interaction for aniline has been introduced by the mutation. Stopped-flow kinetic data show that the restricted heme access in A147Y or A147M slows the reaction between the enzyme and H202, but not to an extent that it becomes rate limiting for the oxidation of the substrates examined. The rate constant for compound ES formation with A147Y is 2.5 times slower than wild-type CCP. These observations strongly support the suggestion that small molecule oxidations occur at sites on the enzyme distinct from those utilized by cytochrome c and that the specificity of small molecule oxidation can be significantly modulated by manipulating access to the heme edge. The results help to define the role of alternative electron transfer pathways in cytochrome c peroxidase and may have useful applications in improving the specificity of peroxidase with engineered function.

Horseradish peroxidase Phe172-->Tyr mutant. Sequential formation of compound I with a porphyrin radical cation and a protein radical

A gene coding for the F172Y mutant of horseradish peroxidase isozyme C (HRP) has been constructed and expressed in both Spodoptera frugiperda (SF-9) and Trichoplusia ni egg cell homogenate (HighFive) cells. Homology modeling with respect to three peroxidases for which crystal structures are available places Phe172 on the proximal side of the heme in the vicinity of porphyrin pyrrole ring C. The pH optimum and spectroscopic properties of the F172Y mutant are essentially identical to those of wild type HRP. Vmax values show that the mutant protein retains most of the guaiacol oxidizing activity. Stopped flow studies indicate that Compound I is formed with H2O2 at the same rate (kappa 1 = 1.6 x 10(7) M-1 s-1) at both pH 6.0 and 8.0 as it is with the wild type enzyme. This Compound I species decays rapidly at a rate kappa 2 = 1.01 s-1, pH 7.0, to a second two-electron oxidized species that retains the ferryl (FeIV = O) absorption. EPR studies establish that a ferryl porphyrin radical cation is present in the initial Compound I, but electron transfer from the protein results in formation of a second Compound I species with an unpaired electron on the protein (presumably on Tyr172). The presence or absence of oxidizable amino acids adjacent to the heme is thus a key determinant of whether the second oxidation equivalent in Compound I is found as a porphyrin or protein radical cation.

Reductions by ferrocytochrome c peroxidase: 5. Kinetics of ferricyanide reduction

The kinetics of reduction of ferricyanide by yeast ferrocytochrome c peroxidase (CPPII) were investigated as a function of ionic strength in phosphate buffers at pH 7.0 and 25 ± 1 °C. The observed bimolecular rate constant (k12) is 8.4 × 104 M−1s−1in 0.1 M phosphate. The dependence of the reaction rate on ionic strength indicates a change of −9 on the protein at pH 7.0, which is in good agreement with the total charge of −11 estimated for CCPIIfrom its amino acid content. Substituting k12at infinite ionic strength [Formula: see text] into the Marcus cross relation yields an electron self-exchange rate constant [Formula: see text] for the FeIII/FeIIcouple of CCP of 7.2 × 10−5 M−1s−1. This value is over four orders of magnitude higher than that calculated for the FeIV/FeIIIcouple of CCP from literature data for cross-reactions with ferrocyanide at pH 7.0. Possible reasons for the large difference in the two CCP [Formula: see text] values are discussed. Literature data also allowed [Formula: see text] values for various other heme proteins to be determined from their cross-reactions with ferricyanide. The calculated rate constants vary by eight orders of magnitude, and the variation of [Formula: see text] with protein structure suggests that the redox reactivity of ferrous heme proteins towards ferricyanide is dependent on the spin state and coordination of iron, as well as on the accessibility of the heme. Keywords: cytochrome c peroxidase, ferricyanide, Marcus cross relation, electron self-exchange.

Arylhydrazines as probes of hemoprotein structure and function

The reactions of arylhydrazines (ArNHNH2) or aryldiazenes (ArN = NH) with simple iron porphyrins or with hemoproteins that have relatively open active sites, including hemoglobin, myoglobin, cytochrome P450, chloroperoxidase, catalase, prostaglandin synthase, and indoleamine-2,3-dioxygenase yield sigma-bonded aryl-iron complexes. Denaturation of the protein complexes under aerobic, acidic conditions shifts the aryl group to the porphyrin nitrogens and produces mixtures of the four possible N-arylprotoporphyrin IX regioisomers. The regioisomers are obtained in approximately equal amounts if the iron-to-nitrogen shift occurs outside of the protein but the ratio of isomers differs if the rearrangement is controlled by the protein. Only in the case of cytochrome P450 enzymes can the shift be induced to occur without denaturation of the protein. The isomer ratios obtained when the shift occurs in the intact active site provide direct experimental information on the active site topology and dynamics. Topological information has thus been obtained for cytochromes P450 1A1, 1A2, 2B1, 2B2, 2B4, 2B10, 2B11, 2E1, 11A1, 51, 101, 102, and 108. In contrast to hemoproteins with open active sites, conventional peroxidases react with arylhydrazines to give delta-meso-aryl adducts and covalent protein adducts. Reaction with the delta-meso edge but not the heme iron provides key evidence that restricting access of substrates to the ferryl oxygen helps direct the reaction towards peroxidase rather than peroxygenase catalysis.

Oxidation of ferrocytochrome c by lignin peroxidase

We demonstrate direct oxidation of ferrocytochrome c by lignin peroxidase (LiP) from the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Steady-state kinetic data fit a peroxidase ping-pong mechanism rather than an ordered bi-bi ping-pong mechanism, suggesting that the reductions of LiP compounds I and II by ferrocytochrome c are irreversible. The pH dependence of the overall reaction apparently is controlled by two factors, the pH dependence of the electron-transfer rate and the pH dependence of enzyme inactivation in the presence of H2O2. In the presence of 100 microM H2O2, veratryl alcohol (VA) significantly enhanced cytochrome c oxidation at pH 3.0 but had little effect above pH 4.5. In the presence of < 10 microM H2O2, the stimulating effect of VA on the reaction is greatly diminished. As with cytochrome c peroxidase reactions, LiP oxidation of ferrocytochrome c decreased as the ionic strength increased, implying the involvement of electrostatic interactions between the polymeric substrate and enzyme. The reaction product ferricytochrome c inhibited VA oxidation by LiP in a noncompetitive manner, suggesting that cytochrome c binds to LiP at a site different from the small aromatic substrate binding site. Recent crystallographic studies show that the heme is buried in the LiP protein and unavailable for direct interaction with polymeric substrates, suggesting that electron transfer from ferrocytochrome c to LiP occurs over a relatively long range. The role of VA in this electron-transfer reaction is discussed.(ABSTRACT TRUNCATED AT 250 WORDS)