Cytochrome P450 Monooxygenases, Chemistry Of: Advanced Article
Cytochrome P450 Monooxygenases, Chemistry Of: Advanced Article
Cytochrome P450 Monooxygenases, Chemistry Of: Advanced Article
Ilia G Denisov,
University of Illinois, Urbana, Illinois
doi: 10.1002/9780470048672.wecb110
Advanced Article
Article Contents
Reactions Catalyzed By Cytochromes P450 Reaction Cycle and Intermediates StructuresCommon Fold and Variations
Cytochromes P450 monooxygenases represent a large superfamily of heme enzymes, which require a dioxygen molecule and two electrons supplied by a NAD(P)H-dependent protein redox partner to form catalytically active high-valent ferryl-oxo intermediate. These heme enzymes are found in most organisms from all biological kingdoms and catalyze various oxidative chemical transformations important for the biosynthesis of steroid hormones, vitamins, signaling molecules, and many other compounds, as well as for the metabolism of xenobiotics.
Cytochromes P450 represent a superfamily of heme enzymes with a common fold and mechanism that requires an atmospheric dioxygen molecule, two electrons from NAD(P)H, and one or two protons available from solvent water to form an active catalytic ferryl-oxo intermediate (1). All cytochromes P450 have one heme b (protoporphyrin IX) buried deeply in the protein globule, with molecular masses in the range 4560 kDa. In the resting state, heme iron is oxidized (Fe3+ ) and is coordinated with the thiolate sulfur atom of cysteine as the fth axial ligand with the sixth position vacant or occupied by water. The iron serves as a sole redox center in the catalytic cycle, which accepts two electrons sequentially and channels them to coordinated dioxygen to form a (hydro)peroxo-ferric intermediate. Second protonation of the distal oxygen atom and transient formation of the iron coordinated oxo-water, FeOOH2 , results in the heterolytic scission of OO bond and formation of the ferryl oxo porphyrin-cation radical, which is termed Compound I, by analogy to the same active intermediate rst documented in peroxidases and catalases (2).
regiospecic and stereospecic mode, to provide the selectivity of the chemical transformation. Thus, the broad range of metabolized substrates and the unprecedented variability of the chemical reactions catalyzed by cytochromes P450 can be attributed largely to the differences in substrate binding properties of different isozymes. With respect to their functional roles in living organisms, cytochromes P450 can be separated tentatively into the enzymes essential for biosynthetic pathways and the xenobiotic metabolizing enzymes (1). The former group includes cytochromes P450 involved into the biosynthesis of steroid hormones, antibiotics, and the transformation of vitamins and cofactors such as retinoids, carotenoids, eicosanoids, and fatty acid derivatives as well as those involved in endogenous intracellular and extracellular signaling. Most reactions are catalyzed with narrow substrate specicity, and they afford products with high regioselectivity and stereoselectivity. As a result, some cytochromes P450 from this group are critical for normal life cycle, and deciencies can lead to serious diseases (7). In contrast, most cytochromes P450 that belong to the latter group can metabolize a variety of substrates of different sizes through multiple chemical mechanisms and even can form several different products from one substrate. Some enzymes may also bind simultaneously two or three substrate molecules, same or different, and various cases of the resulting activation or inhibition of the product turnover were documented both in vivo and in vitro (4, 7). Cytochromes P450 from both groups are represented in all biological kingdoms; although in many cases, the information about their biological functions and underlying chemical mechanisms is incomplete and fragmented at best. Despite the unprecedented variability of chemical reactions catalyzed by cytochromes P450, all the important features of their mechanism can be attributed to the oxidative transformations driven by the main catalytic intermediate, which is a 1
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ferryl-oxo heme complex with the porphyrin pi-cation radical, or Compound I (3, 4, 8). Some important exceptions involve the hydroperoxoferric complex, Compound 0, and perhaps the one-electron reduced Cpd I, ferryl oxo heme complex Compound II (1, 3, 4, 9). Nonclassic reactions catalyzed by some cytochromes P450, which do not use oxygen, and thus deviate from the main P450 mechanism, include direct reductive processes driven by the heme iron (conversion of nitric oxide to nitrous oxide by CYP55, reductive dehalogenation, reduction of azo compounds and quinines, etc.). Another important role of cytochrome P450 activity is that they can react with peroxides with no consumption of external redox equivalents and perform peroxidase-type chemistry with the OO bond scission, or afford rearrangements of fatty acid hydroperoxides.
of Cpd I in the high-spin and low-spin states. The possibility of involvement of Cpd 0, which is the ferric-hydroperoxo intermediate, into the carbon hydroxylation is also debated in the literature, but this species is much weaker oxidant and may participate in catalysis only in rare cases when the barrier for hydroxylation by Cpd 0 is lower than the barrier for the Cpd I formation. Carbon hydroxylation is one of the most common reactions for all cytochromes P450, with substrates that include steroid hormones, fatty acids, vitamins, and antibiotics (5, 11).
Hydroxylation of hydrocarbons
Oxygen atom from Cpd I is inserted into the CH bond of saturated hydrocarbons (Scheme 1a) by means of hydrogen atom abstraction followed by recombination of the transient hydroxyl with the carbon radical [the so-called oxygen rebound mechanism proposed by Groves in 1976 (8, 10)]. Another possibility can be the concerted oxygen insertion into the CH bond. Both pathways are rationalized by the two-state mechanism developed by Shaik et al. (6, 9), which describes different reactivities
(a) C (b) S S+ O N CH3 N H H C O H
(c) C C C
O C
(d) O H (e) C C C C
(f)
H O
O H
Scheme 1 Typical reactions catalyzed by cytochromes P450: (a) hydroxylation of saturated hydrocarbons; (b) heteroatom oxidation and dealkylation; (c) olen epoxidation; (d) aromatic hydroxylation; (e) desaturation; (f) aldehyde deformylation.
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substrate molecule and deviate in this sense from the canonical stoichiometry of P450 monooxygenase catalysis. Desaturation reactions are common in the metabolism of heterocyclic xenobiotics and in biosynthesis of fatty acid derivatives. Aromatase CYP19 also performs a complex desaturation reaction at the third and last step of the transformation of androgens to estrogens. The aromatization reaction of the steroid ring A is catalyzed by the hydroperoxo-ferric intermediate, whereas Cpd I is responsible for the rst two hydroxylation steps of this process.
ROH 7
H2O FeIII
RH
S FeIII oxidase shunt H2O2 O2 autoxidation shunt O (1) O O FeIII H+ S 5a O (2) FeIII S e S
e 3 FeII S O2
O FeIV S + H2O
H+
O Fe
III
S 5b
Figure 1 Catalytic cycle of cytochromes P450. Main path (1) through (7) is shown in bold arrows forming a circle. Uncoupling pathways are shown in dashed lines. Reproduced with permission from the American Chemical Society from Reference 2, p. 2257.
P450 saturated with substrates are reduced much faster than in the substrate-free state because of the positive shifts of the redox potential by 100 mV. Such control over the rate of the rst electron transfer by the substrate binding represents an important feature of the overall steady-state kinetics of many cytochromes P450; although some isozymes exist in a predominantly high-spin state, even without substrates, and they presumably lack this switch. Some cytochromes P450 can bind two or three molecules of substrate or inhibitor simultaneously (CYP107, CYP158A1, CYP158A2, CYP2B4, CYP2C8, CYP3A4, CYP245) and as a result may reveal non-Michaelis turnover kinetics. Functional homotropic and heterotropic cooperativity (i.e., the perturbation of the activity of the enzyme with respect to one substrate molecule by the binding of another molecule of the same or different type, respectively) typically is observed for such cytochromes P450. This allosteric behavior of xenobiotic metabolizing cytochromes P450 constitutes the important aspect of the drugdrug interaction problem in the pharmaceutical and medicinal chemistry and industry.
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bacterial cytochromes P450 and mitochondrial P450 systems. In these systems, the electron transfer from the FAD-containing reductase to the heme enzyme cytochrome P450 is mediated by the soluble iron-sulfur protein ferredoxin. In bacteria, all three proteins are soluble, whereas in mitochondria of eukaryotic cells, cytochromes P450 and reductases are associated with the inner membrane. The systems that belong to the second class include only two proteins, and the cytochrome P450 is reduced directly by the cytochrome P450 reductase (CPR), which contains both FAD and avin mononucleotide. Variations of these systems include fusion enzymes in which a single polypeptide chain folds into two or three domains that correspond to the heme protein, iron-sulfur protein, and/or avoprotein components of cytochrome P450 catalytic system (12). Many CPR avoproteins strongly favor the usage of either NADH or NADPH, whereas some avoproteins can use both efciently. Electron transfer in Class I systems is studied in detail for CYP101 and its redox partner putidaredoxin (2Fe-2S), which contains protein with molecular mass 12.6 kDa. Binding of putidaredoxin at the heme proximal site of CYP101 and formation of the transient electron transfer complex is accompanied by subtle conformational changes of both proteins and concomitant changes in their redox properties that stimulate the reduction of the heme iron to the ferrous state. The complex of CYP101Pd is not very tight (Kd is in micromolar range), because facile dissociation is necessary to maintain the fast overall turnover. However, this complex is highly specic and can be perturbed signicantly by single point mutations at the proteinprotein interface. The apparent rst-order rate of the rst electron transfer in this system measured in kinetic experiments is in the range of 50100 s1 .
difference is caused by the replacement of the mostly conserved alcohol functionality of T252 residue in CYP101 by methyl groups of A245 (CYP107) and A245 in CYP158. The absence of T252 hydroxyl within the hydrogen bond distance to the distal oxygen atom of the coordinated dioxygen is compensated in the latter two enzymes by the specic positioning of hydroxyl groups on the bound substrates, which in turn stabilize water molecules assumed to be the ultimate source of protons for the oxygen activation (see below). Usually, oxygen binding is faster than other steps in the enzymatic cycle, and it is not rate limiting in the overall substrate turnover. However, the lifetime of oxy-ferrous complex in cytochromes P450 at physiologic temperatures is in the range of seconds, because it decomposes spontaneously back to the resting ferric state with the formation of superoxide ion in an autoxidation reaction. Usually, the rate of autoxidation is lower by one or two orders of magnitude for the enzymes saturated with substrate. Higher stability of substrate-bound oxy-ferrous cytochromes P450 is explained in part by their higher redox potentials (i.e., by thermodynamic stabilization of the oxygenated heme enzyme in the enzyme-substrate complex). In addition, the presence of substrates in the active site was shown to impose dynamic constraints on the superoxide escape and to increase the kinetic stability of oxy-ferrous P450. Inhibition of autoxidation is an essential part of the regulatory role played by substrates in the overall optimization of the P450 cycle via minimization of this uncoupling reaction.
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Figure 2 Structure of the human hepatic cytochrome P450 CYP3A4 (18) is shown from the distal site of the heme in cartoon representation. The spacious substrate-binding cavity is represented as a mesh. The heme is shown in sticks, which can be observed under the mesh grid. Helices are labeled by letters according to the common notation for all cytochromes P450 that share the same fold (17). Prepared using PyMol (DeLano Scientic LLC, San Carlos, CA)
based on activation of dioxygen (i.e., nitric oxide reductase CYP55 and CYP152, which uses hydrogen peroxide). Approximately 50% of the residues are located in helical fragments, which are designated by letters A to L with the addition of B, F, G, and J in some isozymes, and 710% are found in small beta-sheets interspersed with exible loops. As compared with the soluble bacterial enzymes, membrane-bound proteins usually have an extra N-terminal fragment that is thought to be incorporated into the membranes and longer loops with one or two small additional helical fragments. The heme (protoporphyrin IX, heme b) is buried in the protein matrix between the long I-helix on the distal side and L helix on the proximal side. The loop at the N-terminus of L-helix contains absolutely conserved cysteinate with the deprotonated sulfur atom that serves as the proximal axial ligand of the heme iron. Three hydrogen bonds with this sulfur atom are formed by the amide groups of the highly conserved neighboring residues. These bonds are necessary to raise the redox potential of cytochrome P450 to the range accessible for the ultimate physiologic reductant NAD(P)H. Hydrogen bonds between propionic carboxyls and the side chains of protein amino acids prevent the loss of the heme and stabilize the native conformation. Another important and highly conserved feature in all structures of cytochromes P450 with only a few exceptions is the 5
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presence of the acid-alcohol pair (i.e., sequential acid and alcohol side chains at the I-helix just next to the dioxygen coordinated to the heme iron). An acidic side chain is provided by Asp or Glu residue (n ), whereas alcohol (n + 1) is from Thr or Ser. The hydroxyl of the latter is very often hydrogen bonded to the peptide carbonyl of the Gly (n 3) forming a kink, which interrupts the regular -helical structure and is thought to be essential for the efcient oxygen activation. Structures of the oxy-ferrous complexes resolved for CYP101, CYP107, and CYP158 reveal the appearance of specically positioned water molecules, which are stabilized by the appropriate rearrangement of the side-chains of the acid-alcohol pair described above. These water molecules play an important role in the directed proton delivery provided by protein for the formation of Compound 0 and Compound I, although the details of the mechanism and specic pathway of this proton delivery are still debated. Helices B, B, F, F, G, and G and connecting loops are involved in substrate binding and in general are much more variable and exible (upper part of the substrate binding cavity shown in Fig. 2). These parts have different length in different classes of P450, with longer disordered insertions typical for eukaryotic enzymes and shorter and more compact structures characteristic for the proteins from extremophilic organisms. In all classes, however, the protein has to experience a large-scale conformational change to open access to the substrate-binding cavity. Comparison of the X-ray structures of cytochromes P450 with and without substrates and the results of molecular dynamics studies suggest that these conformational changes involve concerted movement of the fragments, which form the substrate-binding cavity that includes helices F and G and fragments between them, as well as B and C helices. Such an opening movement was rst observed in the X-ray structures of CYP101 with the wired substrates (19). In these structures, the diaminoalkane chain traced the tentative substrate access channel that connects adamantane positioned in the substrate-binding pocket and the uorescent group on the surface of the protein. However, in many cases, the conformations of cytochromes P450 with the bound substrates or inhibitors are even more compact than in substrate-free state, in which the exible fragments rearrange to provide additional interactions with the hydrophobic molecule bound in the active center. In general, the high plasticity of P450 fold provides basis for their ability to bind multiple organic molecules with different sizes and chemical structures, which is critically important for the efcient metabolism of xenobiotics.
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Further Reading
Bernhardt R. Cytochrome P450: structure, function, and generation of reactive oxygen species. Rev. Physiol. Biochem. Pharmacol. 1996;127:137221. Bernhardt R. Cytochromes P450 as versatile biocatalysts. J. Biotechnol. 2006;124:128145.
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Meunier B, de Visser SP, Shaik S. Mechanism of oxidation reactions catalyzed by cytochrome P450 enzymes. Chem. Rev. 2004;104: 39473980. Ortiz de Montellano PR, ed. Cytochrome P450: Structure, Mechanism, and Biochemistry. 2nd edition. 1995. Plenum Press, New York. Sigel A, Sigel H, Sigel RKO, eds. The Ubiquitous Roles of Cytochrome P450 Proteins, Volume 3: Metal Ions in Life Sciences. 2007. John Wiley & Sons, Ltd., Chichester, UK.
See Also
Drug Metabolizing Enzymes Hemes in Biology Inorganic Chemistry in Biology Metallo-Enzymes and Metallo-Proteins, Chemistry of Oxygen-Activating Enzymes, Chemistry of
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