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2043  structures 4897  species 0  interactions 197545  sequences 2067  architectures

Family: p450 (PF00067)

Summary: Cytochrome P450

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Cytochrome P450
Structure of lanosterol 14 α-demethylase (CYP51).png
Structure of lanosterol 14α-demethylase (CYP51)
Identifiers
Symbolp450
PfamPF00067
InterProIPR001128
PROSITEPDOC00081
SCOPe2cpp / SUPFAM
OPM superfamily39
OPM protein2bdm
Membranome265

Cytochromes P450 (CYPs) are a family of enzymes containing heme as a cofactor that function as monooxygenases.[1] In mammals, these proteins oxidize steroids, fatty acids, and xenobiotics, and are important for the clearance of various compounds, as well as for hormone synthesis and breakdown. In plants, these proteins are important for the biosynthesis of defensive compounds, fatty acids, and hormones.[2]

CYP enzymes have been identified in all kingdoms of life: animals, plants, fungi, protists, bacteria, archaea, and even in viruses.[3] However, they are not omnipresent; for example, they have not been found in Escherichia coli.[4][5] More than 50,000 distinct CYP proteins are known.[6]

CYPs are, in general, the terminal oxidase enzymes in electron transfer chains, broadly categorized as P450-containing systems. The term "P450" is derived from the spectrophotometric peak at the wavelength of the absorption maximum of the enzyme (450 nm) when it is in the reduced state and complexed with carbon monoxide. Most CYPs require a protein partner to deliver one or more electrons to reduce the iron (and eventually molecular oxygen).

Nomenclature

Genes encoding CYP enzymes, and the enzymes themselves, are designated with the root symbol CYP for the superfamily, followed by a number indicating the gene family, a capital letter indicating the subfamily, and another numeral for the individual gene. The convention is to italicise the name when referring to the gene. For example, CYP2E1 is the gene that encodes the enzyme CYP2E1—one of the enzymes involved in paracetamol (acetaminophen) metabolism. The CYP nomenclature is the official naming convention, although occasionally CYP450 or CYP450 is used synonymously. However, some gene or enzyme names for CYPs may differ from this nomenclature, denoting the catalytic activity and the name of the compound used as substrate. Examples include CYP5A1, thromboxane A2 synthase, abbreviated to TBXAS1 (ThromBoXane A2 Synthase 1), and CYP51A1, lanosterol 14-α-demethylase, sometimes unofficially abbreviated to LDM according to its substrate (Lanosterol) and activity (DeMethylation).[7]

The current nomenclature guidelines suggest that members of new CYP families share at least 40% amino acid identity, while members of subfamilies must share at least 55% amino acid identity. There are nomenclature committees that assign and track both base gene names (Cytochrome P450 Homepage) and allele names (CYP Allele Nomenclature Committee).

Classification

Based on the nature of the electron transfer proteins, CYPs can be classified into several groups:[8]

Microsomal P450 systems
in which electrons are transferred from NADPH via cytochrome P450 reductase (variously CPR, POR, or CYPOR). Cytochrome b5 (cyb5) can also contribute reducing power to this system after being reduced by cytochrome b5 reductase (CYB5R).
Mitochondrial P450 systems
which employ adrenodoxin reductase and adrenodoxin to transfer electrons from NADPH to P450.
Bacterial P450 systems
which employ a ferredoxin reductase and a ferredoxin to transfer electrons to P450.
CYB5R/cyb5/P450 systems, in which both electrons required by the CYP come from cytochrome b5.
FMN/Fd/P450 systems
originally found in Rhodococcus species, in which a FMN-domain-containing reductase is fused to the CYP.
P450 only
systems, which do not require external reducing power. Notable ones include thromboxane synthase (CYP5), prostacyclin synthase (CYP8), and CYP74A (allene oxide synthase).

The most common reaction catalyzed by cytochromes P450 is a monooxygenase reaction, e.g., insertion of one atom of oxygen into the aliphatic position of an organic substrate (RH) while the other oxygen atom is reduced to water:

RH + O2 + NADPH + H+ → ROH + H2O + NADP+

Many hydroxylation reactions (insertion of hydroxyl groups) use CYP enzymes.

Mechanism

The "Fe(V) intermediate" at the bottom left is a simplification: it is an Fe(IV) with a radical heme ligand.

Structure

The active site of cytochrome P450 contains a heme-iron center. The iron is tethered to the protein via a cysteine thiolate ligand. This cysteine and several flanking residues are highly conserved in known CYPs and have the formal PROSITE signature consensus pattern [FW] - [SGNH] - x - [GD] - {F} - [RKHPT] - {P} - C - [LIVMFAP] - [GAD].[9] Because of the vast variety of reactions catalyzed by CYPs, the activities and properties of the many CYPs differ in many aspects. In general, the P450 catalytic cycle proceeds as follows:

Catalytic cycle

  1. Substrate binds in proximity to the heme group, on the side opposite to the axial thiolate. Substrate binding induces a change in the conformation of the active site, often displacing a water molecule from the distal axial coordination position of the heme iron,[10] and changing the state of the heme iron from low-spin to high-spin.[11]
  2. Substrate binding induces electron transfer from NAD(P)H via cytochrome P450 reductase or another associated reductase.[12]
  3. Molecular oxygen binds to the resulting ferrous heme center at the distal axial coordination position, initially giving a dioxygen adduct not unlike oxy-myoglobin.
  4. A second electron is transferred, from either cytochrome P450 reductase, ferredoxins, or cytochrome b5, reducing the Fe-O2 adduct to give a short-lived peroxo state.
  5. The peroxo group formed in step 4 is rapidly protonated twice, releasing one molecule of water and forming the highly reactive species referred to as P450 Compound 1 (or just Compound I). This highly reactive intermediate was isolated in 2010,[13] P450 Compound 1 is an iron(IV) oxo (or ferryl) species with an additional oxidizing equivalent delocalized over the porphyrin and thiolate ligands. Evidence for the alternative perferryl iron(V)-oxo [10] is lacking.[13]
  6. Depending on the substrate and enzyme involved, P450 enzymes can catalyze any of a wide variety of reactions. A hypothetical hydroxylation is shown in this illustration. After the product has been released from the active site, the enzyme returns to its original state, with a water molecule returning to occupy the distal coordination position of the iron nucleus.
Oxygen rebound mechanism utilized by cytochrome P450 for conversion of hydrocarbons to alcohols via the action of "compound I", an iron(IV) oxide bound to a heme radical cation.
  1. An alternative route for mono-oxygenation is via the "peroxide shunt" (path "S" in figure). This pathway entails oxidation of the ferric-substrate complex with oxygen-atom donors such as peroxides and hypochlorites.[14] A hypothetical peroxide "XOOH" is shown in the diagram.

Spectroscopy

Binding of substrate is reflected in the spectral properties of the enzyme, with an increase in absorbance at 390 nm and a decrease at 420 nm. This can be measured by difference spectroscopies and is referred to as the "type I" difference spectrum (see inset graph in figure). Some substrates cause an opposite change in spectral properties, a "reverse type I" spectrum, by processes that are as yet unclear. Inhibitors and certain substrates that bind directly to the heme iron give rise to the type II difference spectrum, with a maximum at 430 nm and a minimum at 390 nm (see inset graph in figure). If no reducing equivalents are available, this complex may remain stable, allowing the degree of binding to be determined from absorbance measurements in vitro[14] C: If carbon monoxide (CO) binds to reduced P450, the catalytic cycle is interrupted. This reaction yields the classic CO difference spectrum with a maximum at 450 nm.

P450s in humans

Human CYPs are primarily membrane-associated proteins[15] located either in the inner membrane of mitochondria or in the endoplasmic reticulum of cells. CYPs metabolize thousands of endogenous and exogenous chemicals. Some CYPs metabolize only one (or a very few) substrates, such as CYP19 (aromatase), while others may metabolize multiple substrates. Both of these characteristics account for their central importance in medicine. Cytochrome P450 enzymes are present in most tissues of the body, and play important roles in hormone synthesis and breakdown (including estrogen and testosterone synthesis and metabolism), cholesterol synthesis, and vitamin D metabolism. Cytochrome P450 enzymes also function to metabolize potentially toxic compounds, including drugs and products of endogenous metabolism such as bilirubin, principally in the liver.

The Human Genome Project has identified 57 human genes coding for the various cytochrome P450 enzymes.[16]

Drug metabolism

Proportion of antifungal drugs metabolized by different families of CYPs.[17]

CYPs are the major enzymes involved in drug metabolism, accounting for about 75% of the total metabolism.[18] Most drugs undergo deactivation by CYPs, either directly or by facilitated excretion from the body. Also, many substances are bioactivated by CYPs to form their active compounds like clopidogrel.

Drug interaction

Many drugs may increase or decrease the activity of various CYP isozymes either by inducing the biosynthesis of an isozyme (enzyme induction) or by directly inhibiting the activity of the CYP (enzyme inhibition). A classical example includes anti-epileptic drugs, such as Phenytoin, which induces CYP1A2, CYP2C9, CYP2C19, and CYP3A4.

Effects on CYP isozyme activity are a major source of adverse drug interactions, since changes in CYP enzyme activity may affect the metabolism and clearance of various drugs. For example, if one drug inhibits the CYP-mediated metabolism of another drug, the second drug may accumulate within the body to toxic levels. Hence, these drug interactions may necessitate dosage adjustments or choosing drugs that do not interact with the CYP system. Such drug interactions are especially important to consider when using drugs of vital importance to the patient, drugs with significant side-effects, or drugs with a narrow therapeutic index, but any drug may be subject to an altered plasma concentration due to altered drug metabolism.

Many substrates for CYP3A4 are drugs with a narrow therapeutic index, such as amiodarone[19] or carbamazepine.[20] Because these drugs are metabolized by CYP3A4, the mean plasma levels of these drugs may increase because of enzyme inhibition or decrease because of enzyme induction.

Interaction of other substances

Naturally occurring compounds may also induce or inhibit CYP activity. For example, bioactive compounds found in grapefruit juice and some other fruit juices, including bergamottin, dihydroxybergamottin, and paradicin-A, have been found to inhibit CYP3A4-mediated metabolism of certain medications, leading to increased bioavailability and, thus, the strong possibility of overdosing.[21] Because of this risk, avoiding grapefruit juice and fresh grapefruits entirely while on drugs is usually advised.[22]

Other examples:

Other specific CYP functions

Steroid hormones

Steroidogenesis, showing many of the enzyme activities that are performed by cytochrome P450 enzymes.[30] HSD: Hydroxysteroid dehydrogenase.

A subset of cytochrome P450 enzymes play important roles in the synthesis of steroid hormones (steroidogenesis) by the adrenals, gonads, and peripheral tissue:

Polyunsaturated fatty acids and eicosanoids

Certain cytochrome P450 enzymes are critical in metabolizing polyunsaturated fatty acids (PUFAs) to biologically active, intercellular cell signaling molecules (eicosanoids) and/or metabolize biologically active metabolites of the PUFA to less active or inactive products. These CYPs possess cytochrome P450 omega hydroxylase and/or epoxygenase enzyme activity.

CYP families in humans

Humans have 57 genes and more than 59 pseudogenes divided among 18 families of cytochrome P450 genes and 43 subfamilies.[32] This is a summary of the genes and of the proteins they encode. See the homepage of the cytochrome P450 Nomenclature Committee for detailed information.[16]

Family Function Members Genes pseudogenes
CYP1 drug and steroid (especially estrogen) metabolism, benzo[a]pyrene toxification (forming (+)-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide) 3 subfamilies, 3 genes, 1 pseudogene CYP1A1, CYP1A2, CYP1B1 CYP1D1P
CYP2 drug and steroid metabolism 13 subfamilies, 16 genes, 16 pseudogenes CYP2A6, CYP2A7, CYP2A13, CYP2B6, CYP2C8, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP2F1, CYP2J2, CYP2R1, CYP2S1, CYP2U1, CYP2W1 Too many to list
CYP3 drug and steroid (including testosterone) metabolism 1 subfamily, 4 genes, 4 pseudogenes CYP3A4, CYP3A5, CYP3A7, CYP3A43 CYP3A51P, CYP3A52P, CYP3A54P, CYP3A137P
CYP4 arachidonic acid or fatty acid metabolism 6 subfamilies, 12 genes, 10 pseudogenes CYP4A11, CYP4A22, CYP4B1, CYP4F2, CYP4F3, CYP4F8, CYP4F11, CYP4F12, CYP4F22, CYP4V2, CYP4X1, CYP4Z1 Too many to list
CYP5 thromboxane A2 synthase 1 subfamily, 1 gene CYP5A1
CYP7 bile acid biosynthesis 7-alpha hydroxylase of steroid nucleus 2 subfamilies, 2 genes CYP7A1, CYP7B1
CYP8 varied 2 subfamilies, 2 genes CYP8A1 (prostacyclin synthase), CYP8B1 (bile acid biosynthesis)
CYP11 steroid biosynthesis 2 subfamilies, 3 genes CYP11A1, CYP11B1, CYP11B2
CYP17 steroid biosynthesis, 17-alpha hydroxylase 1 subfamily, 1 gene CYP17A1
CYP19 steroid biosynthesis: aromatase synthesizes estrogen 1 subfamily, 1 gene CYP19A1
CYP20 unknown function 1 subfamily, 1 gene CYP20A1
CYP21 steroid biosynthesis 1 subfamilies, 1 gene, 1 pseudogene CYP21A2 CYP21A1P
CYP24 vitamin D degradation 1 subfamily, 1 gene CYP24A1
CYP26 retinoic acid hydroxylase 3 subfamilies, 3 genes CYP26A1, CYP26B1, CYP26C1
CYP27 varied 3 subfamilies, 3 genes CYP27A1 (bile acid biosynthesis), CYP27B1 (vitamin D3 1-alpha hydroxylase, activates vitamin D3), CYP27C1 (unknown function)
CYP39 7-alpha hydroxylation of 24-hydroxycholesterol 1 subfamily, 1 gene CYP39A1
CYP46 cholesterol 24-hydroxylase 1 subfamily, 1 gene, 1 pseudogene CYP46A1 CYP46A4P
CYP51 cholesterol biosynthesis 1 subfamily, 1 gene, 3 pseudogenes CYP51A1 (lanosterol 14-alpha demethylase) CYP51P1, CYP51P2, CYP51P3

P450s in other species

Animals

Many animals have as many or more CYP genes than humans do. Reported numbers range from 35 genes in the sponge Amphimedon queenslandica to 235 genes in the cephalochordate Branchiostoma floridae.[33] Mice have genes for 101 CYPs, and sea urchins have even more (perhaps as many as 120 genes).[34] Most CYP enzymes are presumed to have monooxygenase activity, as is the case for most mammalian CYPs that have been investigated (except for, e.g., CYP19 and CYP5). Gene and genome sequencing is far outpacing biochemical characterization of enzymatic function, though many genes with close homology to CYPs with known function have been found, giving clues to their functionality.

The classes of CYPs most often investigated in non-human animals are those either involved in development (e.g., retinoic acid or hormone metabolism) or involved in the metabolism of toxic compounds (such as heterocyclic amines or polyaromatic hydrocarbons). Often there are differences in gene regulation or enzyme function of CYPs in related animals that explain observed differences in susceptibility to toxic compounds (ex. canines' inability to metabolize xanthines such as caffeine). Some drugs undergo metabolism in both species via different enzymes, resulting in different metabolites, while other drugs are metabolized in one species but excreted unchanged in another species. For this reason, one species's reaction to a substance is not a reliable indication of the substance's effects in humans. A species of Sonoran Desert Drosophila that uses an upregulated expression of the CYP28A1 gene for detoxification of cacti rot is Drosophila mettleri. Flies of this species have adapted an upregulation of this gene due to exposure of high levels of alkaloids in host plants.

CYPs have been extensively examined in mice, rats, dogs, and less so in zebrafish, in order to facilitate use of these model organisms in drug discovery and toxicology. Recently CYPs have also been discovered in avian species, in particular turkeys, that may turn out to be a useful model for cancer research in humans.[35] CYP1A5 and CYP3A37 in turkeys were found to be very similar to the human CYP1A2 and CYP3A4 respectively, in terms of their kinetic properties as well as in the metabolism of aflatoxin B1.[36]

CYPs have also been heavily studied in insects, often to understand pesticide resistance. For example, CYP6G1 is linked to insecticide resistance in DDT-resistant Drosophila melanogaster[37] and CYP6M2 in the mosquito malaria vector Anopheles gambiae is capable of directly metabolizing pyrethroids.[38]

Microbial

Microbial cytochromes P450 are often soluble enzymes and are involved in diverse metabolic processes. In bacteria the distribution of P450s is very variable with many bacteria having no identified P450s (e.g. E.coli). Some bacteria, predominantly actinomycetes, have numerous P450s (e.g.,[39][40]). Those so far identified are generally involved in either biotransformation of xenobiotic compounds (e.g. CYP105A1 from Streptomyces griseolus metabolizes sulfonylurea herbicides to less toxic derivatives,[41]) or are part of specialised metabolite biosynthetic pathways (e.g. CYP170B1 catalyses production of the sesquiterpenoid albaflavenone in Streptomyces albus,[42]). Although no P450 has yet been shown to be essential in a microbe, the CYP105 family is highly conserved with a representative in every streptomycete genome sequenced so far ([43]). Due to the solubility of bacterial P450 enzymes, they are generally regarded as easier to work with than the predominantly membrane bound eukaryotic P450s. This, combined with the remarkable chemistry they catalyse, has led to many studies using the heterologously expressed proteins in vitro. Few studies have investigated what P450s do in vivo, what the natural substrate(s) are and how P450s contribute to survival of the bacteria in the natural environment.Three examples that have contributed significantly to structural and mechanistic studies are listed here, but many different families exist.

  • Cytochrome P450 cam (CYP101A1) originally from Pseudomonas putida has been used as a model for many cytochromes P450 and was the first cytochrome P450 three-dimensional protein structure solved by X-ray crystallography. This enzyme is part of a camphor-hydroxylating catalytic cycle consisting of two electron transfer steps from putidaredoxin, a 2Fe-2S cluster-containing protein cofactor.
  • Cytochrome P450 eryF (CYP107A1) originally from the actinomycete bacterium Saccharopolyspora erythraea is responsible for the biosynthesis of the antibiotic erythromycin by C6-hydroxylation of the macrolide 6-deoxyerythronolide B.
  • Cytochrome P450 BM3 (CYP102A1) from the soil bacterium Bacillus megaterium catalyzes the NADPH-dependent hydroxylation of several long-chain fatty acids at the ω–1 through ω–3 positions. Unlike almost every other known CYP (except CYP505A1, cytochrome P450 foxy), it constitutes a natural fusion protein between the CYP domain and an electron donating cofactor. Thus, BM3 is potentially very useful in biotechnological applications.[44][45]
  • Cytochrome P450 119 (CYP119A1) isolated from the thermophillic archea Sulfolobus solfataricus [46] has been used in a variety of mechanistic studies.[13] Because thermophillic enzymes evolved to function at high temperatures, they tend to function more slowly at room temperature (if at all) and are therefore excellent mechanistic models.

Fungi

The commonly used azole class antifungal drugs work by inhibition of the fungal cytochrome P450 14α-demethylase. This interrupts the conversion of lanosterol to ergosterol, a component of the fungal cell membrane. (This is useful only because humans' P450 have a different sensitivity; this is how this class of antifungals work.)[47]

Significant research is ongoing into fungal P450s, as a number of fungi are pathogenic to humans (such as Candida yeast and Aspergillus) and to plants.

Cunninghamella elegans is a candidate for use as a model for mammalian drug metabolism.

Plants

Plant cytochrome P450s are involved in a wide range of biosynthetic reactions and target a diverse range of biomolecules. These reactions lead to various fatty acid conjugates, plant hormones, secondary metabolites, lignins, and a variety of defensive compounds.[48] Plant genome annotations suggest that cytochrome P450 genes make up as much as 1% of the plant genes. The number and diversity of P450 genes is responsible, in part, for the multitude of bioactive compounds.[49]

P450s in biotechnology

The remarkable reactivity and substrate promiscuity of P450s have long attracted the attention of chemists.[50] Recent progress towards realizing the potential of using P450s towards difficult oxidations have included: (i) eliminating the need for natural co-factors by replacing them with inexpensive peroxide containing molecules,[51] (ii) exploring the compatibility of P450s with organic solvents,[52] and (iii) the use of small, non-chiral auxiliaries to predictably direct P450 oxidation.[citation needed]

InterPro subfamilies

InterPro subfamilies:

Clozapine, imipramine, paracetamol, phenacetin Heterocyclic aryl amines Inducible and CYP1A2 5-10% deficient oxidize uroporphyrinogen to uroporphyrin (CYP1A2) in heme metabolism, but they may have additional undiscovered endogenous substrates. are inducible by some polycyclic hydrocarbons, some of which are found in cigarette smoke and charred food.

These enzymes are of interest, because in assays, they can activate compounds to carcinogens. High levels of CYP1A2 have been linked to an increased risk of colon cancer. Since the 1A2 enzyme can be induced by cigarette smoking, this links smoking with colon cancer.[53]

See also

References

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  37. ^ McCart C, Ffrench-Constant RH (June 2008). "Dissecting the insecticide-resistance- associated cytochrome P450 gene Cyp6g1". Pest Management Science. 64 (6): 639–45. doi:10.1002/ps.1567. PMID 18338338.
  38. ^ Ismail, Hanafy; O'Neill, Paul; Hong, David; Finn, Robert; Henderson, Colin; Wright, Aaron; Cravatt, Benjamin; Hemingway, Janet; Paine, Mark (3 December 2013). "Pyrethroid activity-based probes for profiling cytochrome P450 activities associated with insecticide interactions". PNAS. 110 (49): 19766–19771. doi:10.1073/pnas.1320185110. PMC 3856776. PMID 24248381.
  39. ^ McLean KJ, Clift D, Lewis DG, Sabri M, Balding PR, Sutcliffe MJ, Leys D, Munro AW (May 2006). "The preponderance of P450s in the Mycobacterium tuberculosis genome". Trends in Microbiology. 14 (5): 220–8. doi:10.1016/j.tim.2006.03.002. PMID 16581251.
  40. ^ Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S (May 2003). "Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis". Nature Biotechnology. 21 (5): 526–31. doi:10.1038/nbt820. PMID 12692562.
  41. ^ Leto, O'Keefe (1988). "Identification of constitutive and herbicide inducible cytochromes P-450 in Streptomyces griseolus". Arch Microbiol. 149 (5): 406–12. doi:10.1007/BF00425579.
  42. ^ Moody SC, Zhao B, Lei L, Nelson DR, Mullins JG, Waterman MR, Kelly SL, Lamb DC (May 2012). "Investigating conservation of the albaflavenone biosynthetic pathway and CYP170 bifunctionality in streptomycetes". The FEBS Journal. 279 (9): 1640–9. doi:10.1111/j.1742-4658.2011.08447.x. PMID 22151149.
  43. ^ Moody SC, Loveridge EJ (December 2014). "CYP105-diverse structures, functions and roles in an intriguing family of enzymes in Streptomyces". Journal of Applied Microbiology. 117 (6): 1549–63. doi:10.1111/jam.12662. PMC 4265290. PMID 25294646.
  44. ^ Narhi LO, Fulco AJ (June 1986). "Characterization of a catalytically self-sufficient 119,000-dalton cytochrome P-450 monooxygenase induced by barbiturates in Bacillus megaterium". The Journal of Biological Chemistry. 261 (16): 7160–9. PMID 3086309.
  45. ^ Girvan HM, Waltham TN, Neeli R, Collins HF, McLean KJ, Scrutton NS, Leys D, Munro AW (December 2006). "Flavocytochrome P450 BM3 and the origin of CYP102 fusion species". Biochemical Society Transactions. 34 (Pt 6): 1173–7. doi:10.1042/BST0341173. PMID 17073779.
  46. ^ Wright RL, Harris K, Solow B, White RH, Kennelly PJ (April 1996). "Cloning of a potential cytochrome P450 from the archaeon Sulfolobus solfataricus". FEBS Letters. 384 (3): 235–9. doi:10.1016/0014-5793(96)00322-5. PMID 8617361.
  47. ^ Vanden Bossche H, Marichal P, Gorrens J, Coene MC (September 1990). "Biochemical basis for the activity and selectivity of oral antifungal drugs". British Journal of Clinical Practice. Supplement. 71: 41–6. PMID 2091733.
  48. ^ Schuler MA, Werck-Reichhart D (2003-01-01). "Functional genomics of P450s". Annual Review of Plant Biology. 54 (1): 629–67. doi:10.1146/annurev.arplant.54.031902.134840. PMID 14503006.
  49. ^ Mizutani M, Sato F (March 2011). "Unusual P450 reactions in plant secondary metabolism". Archives of Biochemistry and Biophysics. P450 Catalysis Mechanisms. 507 (1): 194–203. doi:10.1016/j.abb.2010.09.026. PMID 20920462.
  50. ^ Chefson A, Auclair K (October 2006). "Progress towards the easier use of P450 enzymes". Molecular BioSystems. 2 (10): 462–9. doi:10.1039/b607001a. PMID 17216026.
  51. ^ Chefson A, Zhao J, Auclair K (June 2006). "Replacement of natural cofactors by selected hydrogen peroxide donors or organic peroxides results in improved activity for CYP3A4 and CYP2D6". ChemBioChem. 7 (6): 916–9. doi:10.1002/cbic.200600006. PMID 16671126.
  52. ^ Chefson A, Auclair K (July 2007). "CYP3A4 activity in the presence of organic cosolvents, ionic liquids, or water-immiscible organic solvents". ChemBioChem. 8 (10): 1189–97. doi:10.1002/cbic.200700128. PMID 17526062.
  53. ^ Petros WP, Younis IR, Ford JN, Weed SA (October 2012). "Effects of tobacco smoking and nicotine on cancer treatment". Pharmacotherapy. 32 (10): 920–31. doi:10.1002/j.1875-9114.2012.01117. PMC 3499669. PMID 23033231.

Further reading

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cytochrome P450 Provide feedback

Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures [6].

Literature references

  1. Graham-Lorence S, Amarneh B, White RE, Peterson JA, Simpson ER; , Protein Sci 1995;4:1065-1080.: A three-dimensional model of aromatase cytochrome P450. PUBMED:7549871 EPMC:7549871

  2. Degtyarenko KN, Archakov AI; , FEBS Lett 1993;332:1-8.: Molecular evolution of P450 superfamily and P450-containing monooxygenase systems. PUBMED:8405421 EPMC:8405421

  3. Nelson DR, Kamataki T, Waxman DJ, Guengerich FP, Estabrook RW, Feyereisen R, Gonzalez FJ, Coon MJ, Gunsalus IC, Gotoh O, et al; , DNA Cell Biol 1993;12:1-51.: The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature. PUBMED:7678494 EPMC:7678494

  4. Guengerich FP; , J Biol Chem 1991;266:10019-10022.: Reactions and significance of cytochrome P-450 enzymes. PUBMED:2037557 EPMC:2037557

  5. Nebert DW, Gonzalez FJ; , Annu Rev Biochem 1987;56:945-993.: P450 genes: structure, evolution, and regulation. PUBMED:3304150 EPMC:3304150

  6. Werck-Reichhart D, Feyereisen R; , Genome Biol 2000;1:REVIEWS3003.: Cytochromes P450: a success story. PUBMED:11178272 EPMC:11178272


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001128

Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).

Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [ PUBMED:17023115 ], which has haem and flavin domains.

Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.

Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [ PUBMED:16042601 , PUBMED:15128046 , PUBMED:8637843 ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.

This family also includes germacrene A hydroxylase (GAO1; EC 1.14.14.95) from plants such as lettuce (Lactuca sativa). GAO1 is required for the biosynthesis of germacrene-derived sesquiterpene lactones, which are characteristic natural products in members of the Asteraceae [ PUBMED:20351109 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(50)
Full
(197545)
Representative proteomes UniProt
(394200)
RP15
(26765)
RP35
(90718)
RP55
(163058)
RP75
(235808)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(50)
Full
(197545)
Representative proteomes UniProt
(394200)
RP15
(26765)
RP35
(90718)
RP55
(163058)
RP75
(235808)
Alignment:
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Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(50)
Full
(197545)
Representative proteomes UniProt
(394200)
RP15
(26765)
RP35
(90718)
RP55
(163058)
RP75
(235808)
Raw Stockholm Download     Download          
Gzipped Download     Download          

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Overington and HMM_iterative_training
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Eddy SR
Number in seed: 50
Number in full: 197545
Average length of the domain: 338.20 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 78.51 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 463
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the p450 domain has been found. There are 2043 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A087WPC3 View 3D Structure Click here
A0A087WS15 View 3D Structure Click here
A0A087X1C5 View 3D Structure Click here
A0A087X1C5 View 3D Structure Click here
A0A096PQR7 View 3D Structure Click here
A0A0G2JTQ9 View 3D Structure Click here
A0A0G2JTR5 View 3D Structure Click here
A0A0G2JYL7 View 3D Structure Click here
A0A0G2K2P4 View 3D Structure Click here
A0A0G2K339 View 3D Structure Click here
A0A0G2K339 View 3D Structure Click here
A0A0G2K5S9 View 3D Structure Click here
A0A0G2K776 View 3D Structure Click here
A0A0G2KAI3 View 3D Structure Click here
A0A0M7RF98 View 3D Structure Click here
A0A0N4SU47 View 3D Structure Click here
A0A0N7KCX4 View 3D Structure Click here
A0A0N7KDA0 View 3D Structure Click here
A0A0N7KDK7 View 3D Structure Click here
A0A0N7KDP0 View 3D Structure Click here
A0A0N7KFC2 View 3D Structure Click here
A0A0N7KJJ5 View 3D Structure Click here
A0A0N7KLQ6 View 3D Structure Click here
A0A0N7KMG3 View 3D Structure Click here
A0A0N7KPH1 View 3D Structure Click here
A0A0N7KQV8 View 3D Structure Click here
A0A0P0UWT2 View 3D Structure Click here
A0A0P0UZQ2 View 3D Structure Click here
A0A0P0V0F6 View 3D Structure Click here
A0A0P0V315 View 3D Structure Click here
A0A0P0V3S5 View 3D Structure Click here
A0A0P0V5G6 View 3D Structure Click here
A0A0P0V5H7 View 3D Structure Click here
A0A0P0V5J0 View 3D Structure Click here
A0A0P0V5J0 View 3D Structure Click here
A0A0P0V708 View 3D Structure Click here
A0A0P0V748 View 3D Structure Click here
A0A0P0V748 View 3D Structure Click here
A0A0P0V9R1 View 3D Structure Click here
A0A0P0VD21 View 3D Structure Click here
A0A0P0VD68 View 3D Structure Click here
A0A0P0VFK0 View 3D Structure Click here
A0A0P0VFQ1 View 3D Structure Click here
A0A0P0VFQ4 View 3D Structure Click here
A0A0P0VFR0 View 3D Structure Click here
A0A0P0VFT7 View 3D Structure Click here
A0A0P0VFT7 View 3D Structure Click here
A0A0P0VGF6 View 3D Structure Click here
A0A0P0VGG0 View 3D Structure Click here
A0A0P0VIT4 View 3D Structure Click here
A0A0P0VJ99 View 3D Structure Click here
A0A0P0VJA0 View 3D Structure Click here
A0A0P0VJA4 View 3D Structure Click here
A0A0P0VJC6 View 3D Structure Click here
A0A0P0VJD6 View 3D Structure Click here
A0A0P0VJE3 View 3D Structure Click here
A0A0P0VJE3 View 3D Structure Click here
A0A0P0VLE3 View 3D Structure Click here
A0A0P0VSU7 View 3D Structure Click here
A0A0P0VSY0 View 3D Structure Click here
A0A0P0VVF7 View 3D Structure Click here
A0A0P0VVJ1 View 3D Structure Click here
A0A0P0VXV8 View 3D Structure Click here
A0A0P0VXW6 View 3D Structure Click here
A0A0P0VYL2 View 3D Structure Click here
A0A0P0VYR5 View 3D Structure Click here
A0A0P0VZB6 View 3D Structure Click here
A0A0P0W0R0 View 3D Structure Click here
A0A0P0W1B4 View 3D Structure Click here
A0A0P0W5G8 View 3D Structure Click here
A0A0P0W704 View 3D Structure Click here
A0A0P0W7N0 View 3D Structure Click here
A0A0P0WBY2 View 3D Structure Click here
A0A0P0WD92 View 3D Structure Click here
A0A0P0WJA6 View 3D Structure Click here
A0A0P0WM68 View 3D Structure Click here
A0A0P0WM73 View 3D Structure Click here
A0A0P0WME8 View 3D Structure Click here
A0A0P0WMF4 View 3D Structure Click here
A0A0P0WTY0 View 3D Structure Click here
A0A0P0WUZ0 View 3D Structure Click here
A0A0P0WUZ0 View 3D Structure Click here
A0A0P0WWU1 View 3D Structure Click here
A0A0P0WXA8 View 3D Structure Click here
A0A0P0WY46 View 3D Structure Click here
A0A0P0WZ54 View 3D Structure Click here
A0A0P0WZ62 View 3D Structure Click here
A0A0P0WZ65 View 3D Structure Click here
A0A0P0WZ86 View 3D Structure Click here
A0A0P0WZH2 View 3D Structure Click here
A0A0P0WZJ2 View 3D Structure Click here
A0A0P0WZQ4 View 3D Structure Click here
A0A0P0X402 View 3D Structure Click here
A0A0P0X4A3 View 3D Structure Click here
A0A0P0X4L9 View 3D Structure Click here
A0A0P0X5B5 View 3D Structure Click here
A0A0P0X5J7 View 3D Structure Click here
A0A0P0X5K5 View 3D Structure Click here
A0A0P0X5N5 View 3D Structure Click here
A0A0P0X614 View 3D Structure Click here
A0A0P0X631 View 3D Structure Click here
A0A0P0X6L5 View 3D Structure Click here
A0A0P0X6Q2 View 3D Structure Click here
A0A0P0X743 View 3D Structure Click here
A0A0P0X7H0 View 3D Structure Click here
A0A0P0X7M6 View 3D Structure Click here
A0A0P0X842 View 3D Structure Click here
A0A0P0XAP4 View 3D Structure Click here
A0A0P0XAQ5 View 3D Structure Click here
A0A0P0XAQ5 View 3D Structure Click here
A0A0P0XAX3 View 3D Structure Click here
A0A0P0XBR4 View 3D Structure Click here
A0A0P0XD48 View 3D Structure Click here
A0A0P0XI45 View 3D Structure Click here
A0A0P0XJ71 View 3D Structure Click here
A0A0P0XL07 View 3D Structure Click here
A0A0P0XMQ9 View 3D Structure Click here
A0A0P0XMS3 View 3D Structure Click here
A0A0P0XPF8 View 3D Structure Click here
A0A0P0XPF8 View 3D Structure Click here
A0A0P0XRF4 View 3D Structure Click here
A0A0P0XRX9 View 3D Structure Click here
A0A0P0XS22 View 3D Structure Click here
A0A0P0XT35 View 3D Structure Click here
A0A0P0XT48 View 3D Structure Click here
A0A0P0XTA7 View 3D Structure Click here
A0A0P0XTH1 View 3D Structure Click here
A0A0P0XVA7 View 3D Structure Click here
A0A0P0XVK5 View 3D Structure Click here
A0A0P0XW68 View 3D Structure Click here
A0A0P0XW95 View 3D Structure Click here
A0A0P0XWQ5 View 3D Structure Click here
A0A0P0XWS4 View 3D Structure Click here
A0A0P0XWU9 View 3D Structure Click here
A0A0P0XX49 View 3D Structure Click here
A0A0P0XYR6 View 3D Structure Click here
A0A0P0Y224 View 3D Structure Click here
A0A0P0Y232 View 3D Structure Click here
A0A0P0Y4U3 View 3D Structure Click here
A0A0P0Y7X8 View 3D Structure Click here
A0A0P0YC40 View 3D Structure Click here
A0A0P0YD70 View 3D Structure Click here
A0A0P0YD70 View 3D Structure Click here
A0A0R0EBT8 View 3D Structure Click here
A0A0R0EDB8 View 3D Structure Click here
A0A0R0EDG9 View 3D Structure Click here
A0A0R0EDH9 View 3D Structure Click here
A0A0R0EFN4 View 3D Structure Click here
A0A0R0EGB3 View 3D Structure Click here
A0A0R0EGK4 View 3D Structure Click here
A0A0R0EGS3 View 3D Structure Click here
A0A0R0EGW1 View 3D Structure Click here
A0A0R0EH04 View 3D Structure Click here
A0A0R0EJ51 View 3D Structure Click here
A0A0R0EN22 View 3D Structure Click here
A0A0R0ENX8 View 3D Structure Click here
A0A0R0EQV9 View 3D Structure Click here
A0A0R0EQV9 View 3D Structure Click here
A0A0R0ESC4 View 3D Structure Click here
A0A0R0EVS7 View 3D Structure Click here
A0A0R0EXR8 View 3D Structure Click here
A0A0R0EXW4 View 3D Structure Click here
A0A0R0EXW4 View 3D Structure Click here
A0A0R0F2P4 View 3D Structure Click here
A0A0R0F9S7 View 3D Structure Click here
A0A0R0FE08 View 3D Structure Click here
A0A0R0FE21 View 3D Structure Click here
A0A0R0FIB6 View 3D Structure Click here
A0A0R0FIL2 View 3D Structure Click here
A0A0R0FKT2 View 3D Structure Click here
A0A0R0FNB2 View 3D Structure Click here
A0A0R0FNB4 View 3D Structure Click here
A0A0R0FRM9 View 3D Structure Click here
A0A0R0FRM9 View 3D Structure Click here
A0A0R0FVX1 View 3D Structure Click here
A0A0R0FXX4 View 3D Structure Click here
A0A0R0FY29 View 3D Structure Click here
A0A0R0FZC0 View 3D Structure Click here
A0A0R0G2C0 View 3D Structure Click here
A0A0R0G7V8 View 3D Structure Click here
A0A0R0GAK6 View 3D Structure Click here
A0A0R0GB80 View 3D Structure Click here
A0A0R0GB80 View 3D Structure Click here
A0A0R0GCR2 View 3D Structure Click here
A0A0R0GE25 View 3D Structure Click here
A0A0R0GF97 View 3D Structure Click here
A0A0R0GFM6 View 3D Structure Click here
A0A0R0GFM6 View 3D Structure Click here
A0A0R0GJG3 View 3D Structure Click here
A0A0R0GPC6 View 3D Structure Click here
A0A0R0GTI2 View 3D Structure Click here
A0A0R0H2Z4 View 3D Structure Click here
A0A0R0H5X1 View 3D Structure Click here
A0A0R0HCC8 View 3D Structure Click here
A0A0R0HCQ0 View 3D Structure Click here
A0A0R0HCV4 View 3D Structure Click here
A0A0R0HCV4 View 3D Structure Click here
A0A0R0HDD4 View 3D Structure Click here
A0A0R0HFF1 View 3D Structure Click here
A0A0R0HI11 View 3D Structure Click here
A0A0R0HJS7 View 3D Structure Click here
A0A0R0HRZ2 View 3D Structure Click here
A0A0R0HRZ3 View 3D Structure Click here
A0A0R0HRZ3 View 3D Structure Click here
A0A0R0HUC4 View 3D Structure Click here
A0A0R0HVV7 View 3D Structure Click here
A0A0R0HWV7 View 3D Structure Click here
A0A0R0HY73 View 3D Structure Click here
A0A0R0HYP7 View 3D Structure Click here
A0A0R0I0A2 View 3D Structure Click here
A0A0R0I0U7 View 3D Structure Click here
A0A0R0I1Q4 View 3D Structure Click here
A0A0R0I304 View 3D Structure Click here
A0A0R0I598 View 3D Structure Click here
A0A0R0I6S7 View 3D Structure Click here
A0A0R0I8E4 View 3D Structure Click here
A0A0R0I8E9 View 3D Structure Click here
A0A0R0IA67 View 3D Structure Click here
A0A0R0IA67 View 3D Structure Click here
A0A0R0IDL1 View 3D Structure Click here
A0A0R0IE06 View 3D Structure Click here
A0A0R0IE90 View 3D Structure Click here
A0A0R0IE90 View 3D Structure Click here
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