Cytochrome P450

Last updated
Cytochrome P450
Structure of lanosterol 14 a-demethylase (CYP51).png
Structure of lanosterol 14α-demethylase (CYP51)
Identifiers
Symbolp450
Pfam PF00067
InterPro IPR001128
PROSITE PDOC00081
SCOP2 2cpp / SCOPe / SUPFAM
OPM superfamily 39
OPM protein 2bdm
CDD cd00302
Membranome 265
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

Cytochromes P450 (P450s or CYPs) are a superfamily of enzymes containing heme as a cofactor that mostly, but not exclusively, function as monooxygenases. [1] However, they are not omnipresent; for example, they have not been found in Escherichia coli . [2] In mammals, these enzymes oxidize steroids, fatty acids, xenobiotics, and participate in many biosyntheses. [1] By hydroxylation, CYP450 enzymes convert xenobiotics into hydrophilic derivatives, which are more readily excreted.

Contents

P450s 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 P450s require a protein partner to deliver one or more electrons to reduce the iron (and eventually molecular oxygen).

Nomenclature

Genes encoding P450 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 italicize 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. These names should never be used as according to the nomenclature convention (as they denote a P450 in family number 450). However, some gene or enzyme names for P450s are also referred to by historical names (e.g. P450BM3 for CYP102A1) or functional names, denoting the catalytic activity and the name of the compound used as substrate. Examples include CYP5A1, thromboxane A2 synthase, abbreviated to TBXAS1 (ThromBoXane A2Synthase 1), and CYP51A1, lanosterol 14-α-demethylase, sometimes unofficially abbreviated to LDM according to its substrate (Lanosterol) and activity (DeMethylation). [3]

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. Nomenclature committees assign and track both base gene names (Cytochrome P450 Homepage Archived 2010-06-27 at the Wayback Machine ) and allele names (CYP Allele Nomenclature Committee). [4] [5]

Classification

Based on the nature of the electron transfer proteins, P450s can be classified into several groups: [6]

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, but many other hydroxylases exist. Alpha-ketoglutarate-dependent hydroxylases also rely on an Fe=O intermediate but lack hemes. Methane monooxygenase, which converts methane to methanol, are non-heme iron-and iron-copper-based enzymes. [7]

Mechanism

The "Fe(V) intermediate" at the bottom left is a simplification: it is an Fe(IV) with a radical heme ligand. P450cycle.svg
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 P450s, and have the formal PROSITE signature consensus pattern [FW] - [SGNH] - x - [GD] - {F} - [RKHPT] - {P} - C - [LIVMFAP] - [GAD]. [8] 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, [9] and changing the state of the heme iron from low-spin to high-spin. [10]
  2. Substrate binding induces electron transfer from NAD(P)H via cytochrome P450 reductase or another associated reductase, [11] converting Fe(III) to Fe(II).
  3. Molecular oxygen binds to the resulting ferrous heme center at the distal axial coordination position, initially giving a dioxygen adduct similar to 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, [12] 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 [9] is lacking. [12]
  6. Depending on the substrate and enzyme involved, P450 enzymes can catalyze any of a wide variety of reactions. A hypothetical hydroxylation is illustrated. After the hydroxylated 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. FeIVO 2.tif
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. [13] A hypothetical peroxide "XOOH" is shown in the diagram.

Mechanistic details, including the oxygen rebound mechanism, have been investigated with synthetic analogues, consisting of iron oxo heme complexes. [14]

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 [13] 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. However, the interruptive and inhibitory effects of CO varies upon different CYPs such that the CYP3A family is relatively less affected. [15] [16]

See also

Further reading

Related Research Articles

<span class="mw-page-title-main">Cytochrome</span> Redox-active proteins containing a heme with a Fe atom as a cofactor

Cytochromes are redox-active proteins containing a heme, with a central iron (Fe) atom at its core, as a cofactor. They are involved in the electron transport chain and redox catalysis. They are classified according to the type of heme and its mode of binding. Four varieties are recognized by the International Union of Biochemistry and Molecular Biology (IUBMB), cytochromes a, cytochromes b, cytochromes c and cytochrome d.

<span class="mw-page-title-main">Heme</span> Chemical coordination complex of an iron ion chelated to a porphyrin

Heme, or haem, is a ring-shaped iron-containing molecular component of hemoglobin, which is necessary to bind oxygen in the bloodstream. It is composed of four pyrrole rings with 2 vinyl and 2 propionic acid side chains. Heme is biosynthesized in both the bone marrow and the liver.

<span class="mw-page-title-main">CYP2E1</span> Protein-coding gene in the species Homo sapiens

Cytochrome P450 2E1 is a member of the cytochrome P450 mixed-function oxidase system, which is involved in the metabolism of xenobiotics in the body. This class of enzymes is divided up into a number of subcategories, including CYP1, CYP2, and CYP3, which as a group are largely responsible for the breakdown of foreign compounds in mammals.

Ferredoxins are iron–sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied to the "iron protein" first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic bacterium Clostridium pasteurianum.

<span class="mw-page-title-main">Flavin adenine dinucleotide</span> Redox-active coenzyme

In biochemistry, flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins, which is involved with several enzymatic reactions in metabolism. A flavoprotein is a protein that contains a flavin group, which may be in the form of FAD or flavin mononucleotide (FMN). Many flavoproteins are known: components of the succinate dehydrogenase complex, α-ketoglutarate dehydrogenase, and a component of the pyruvate dehydrogenase complex.

Iron–sulfur proteins are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur clusters are found in a variety of metalloproteins, such as the ferredoxins, as well as NADH dehydrogenase, hydrogenases, coenzyme Q – cytochrome c reductase, succinate – coenzyme Q reductase and nitrogenase. Iron–sulfur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe–S clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally, some Fe–S proteins regulate gene expression. Fe–S proteins are vulnerable to attack by biogenic nitric oxide, forming dinitrosyl iron complexes. In most Fe–S proteins, the terminal ligands on Fe are thiolate, but exceptions exist.

<span class="mw-page-title-main">Thromboxane-A synthase</span> Mammalian protein found in Homo sapiens

Thromboxane A synthase 1 , also known as TBXAS1, is a cytochrome P450 enzyme that, in humans, is encoded by the TBXAS1 gene.

Any enzyme system that includes cytochrome P450 protein or domain can be called a P450-containing system.

<span class="mw-page-title-main">Rubredoxin</span> Class of iron-containing proteins

Rubredoxins are a class of low-molecular-weight iron-containing proteins found in sulfur-metabolizing bacteria and archaea. Sometimes rubredoxins are classified as iron-sulfur proteins; however, in contrast to iron-sulfur proteins, rubredoxins do not contain inorganic sulfide. Like cytochromes, ferredoxins and Rieske proteins, rubredoxins are thought to participate in electron transfer in biological systems. Recent work in bacteria and algae have led to the hypothesis that some rubredoxins may instead have a role in delivering iron to metalloproteins.

Nitrite reductase refers to any of several classes of enzymes that catalyze the reduction of nitrite. There are two classes of NIR's. A multi haem enzyme reduces NO2− to a variety of products. Copper containing enzymes carry out a single electron transfer to produce nitric oxide.

<span class="mw-page-title-main">Camphor 5-monooxygenase</span>

In enzymology, a camphor 5-monooxygenase (EC 1.14.15.1) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Cholesterol 24-hydroxylase</span> Protein family

Cholesterol 24-hydroxylase, also commonly known as cholesterol 24S-hydroxylase, cholesterol 24-monooxygenase, CYP46, or CYP46A1, is an enzyme that catalyzes the conversion of cholesterol to 24S-hydroxycholesterol. It is responsible for the majority of cholesterol turnover in the human central nervous system. The systematic name of this enzyme class is cholesterol,NADPH:oxygen oxidoreductase (24-hydroxylating).

<span class="mw-page-title-main">Adrenodoxin reductase</span> Protein-coding gene in the species Homo sapiens

Adrenodoxin reductase, was first isolated from bovine adrenal cortex where it functions as the first enzyme in the mitochondrial P450 systems that catalyze essential steps in steroid hormone biosynthesis. Examination of complete genome sequences revealed that adrenodoxin reductase gene is present in most metazoans and prokaryotes.

Flavoprotein pyridine nucleotide cytochrome reductases catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin-NADP+ reductases, plant and fungal NAD(P)H:nitrate reductases, cytochrome b5 reductases, cytochrome P450 reductases, sulphite reductases, nitric oxide synthases, phthalate dioxygenase reductase, and various other flavoproteins.

<span class="mw-page-title-main">(+)-Menthofuran synthase</span> Class of enzymes

(+)-Menthofuran synthase (EC 1.14.13.104, menthofuran synthase, (+)-pulegone 9-hydroxylase, (+)-MFS, cytochrome P450 menthofuran synthase) is an enzyme with systematic name (+)-pulegone,NADPH:oxygen oxidoreductase (9-hydroxylating). This enzyme catalyses the following chemical reaction

Cytochrome P450 omega hydroxylases, also termed cytochrome P450 ω-hydroxylases, CYP450 omega hydroxylases, CYP450 ω-hydroxylases, CYP omega hydroxylase, CYP ω-hydroxylases, fatty acid omega hydroxylases, cytochrome P450 monooxygenases, and fatty acid monooxygenases, are a set of cytochrome P450-containing enzymes that catalyze the addition of a hydroxyl residue to a fatty acid substrate. The CYP omega hydroxylases are often referred to as monoxygenases; however, the monooxygenases are CYP450 enzymes that add a hydroxyl group to a wide range of xenobiotic and naturally occurring endobiotic substrates, most of which are not fatty acids. The CYP450 omega hydroxylases are accordingly better viewed as a subset of monooxygenases that have the ability to hydroxylate fatty acids. While once regarded as functioning mainly in the catabolism of dietary fatty acids, the omega oxygenases are now considered critical in the production or break-down of fatty acid-derived mediators which are made by cells and act within their cells of origin as autocrine signaling agents or on nearby cells as paracrine signaling agents to regulate various functions such as blood pressure control and inflammation.

This article covers protein engineering of cytochrome (CYP) P450 enzymes. P450s are involved in a range of biochemical catabolic and anabolic process. Natural P450s can perform several different types of chemical reactions including hydroxylations, N,O,S-dealkylations, epoxidations, sulfoxidations, aryl-aryl couplings, ring contractions and expansions, oxidative cyclizations, alcohol/aldehyde oxidations, desaturations, nitrogen oxidations, decarboxylations, nitrations, as well as oxidative and reductive dehalogenations. Engineering efforts often strive for 1) improved stability 2) improved activity 3) improved substrate scope 4) enabled ability to catalyze unnatural reactions. P450 engineering is an emerging field in the areas of chemical biology and synthetic organic chemistry (chemoenzymatic).

<span class="mw-page-title-main">Cytochrome P450 aromatic O-demethylase</span>

Cytochrome P450 aromatic O-demethylase is a bacterial enzyme that catalyzes the demethylation of lignin and various lignols. The net reaction follows the following stoichiometry, illustrated with a generic methoxy arene:

In biochemistry, cytochrome P450 enzymes have been identified in all kingdoms of life: animals, plants, fungi, protists, bacteria, and archaea, as well as in viruses. As of 2018, more than 300,000 distinct CYP proteins are known.

References

  1. 1 2 "Cytochrome P450". InterPro.
  2. ↑ Danielson PB (December 2002). "The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans". Current Drug Metabolism. 3 (6): 561–597. doi:10.2174/1389200023337054. PMID   12369887.
  3. ↑ "NCBI sequence viewer" . Retrieved 2007-11-19.
  4. ↑ Nelson DR (October 2009). "The cytochrome p450 homepage". Human Genomics. 4 (1): 59–65. doi: 10.1186/1479-7364-4-1-59 . PMC   3500189 . PMID   19951895.
  5. ↑ Nelson DR (January 2011). "Progress in tracing the evolutionary paths of cytochrome P450". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1814 (1): 14–18. doi:10.1016/j.bbapap.2010.08.008. PMID   20736090.
  6. ↑ Hanukoglu I (1996). "Electron transfer proteins of cytochrome P450 systems" (PDF). Adv. Mol. Cell Biol. Advances in Molecular and Cell Biology. 14: 29–55. doi:10.1016/S1569-2558(08)60339-2. ISBN   978-0-7623-0113-3.
  7. ↑ Tucci FJ, Rosenzweig AC (February 2024). "Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases". Chemical Reviews. 124 (3): 1288–1320. doi:10.1021/acs.chemrev.3c00727. PMC   10923174 . PMID   38305159.
  8. ↑ Archived 2019-10-18 at the Wayback Machine PROSITE consensus pattern for P450
  9. 1 2 Meunier B, de Visser SP, Shaik S (September 2004). "Mechanism of oxidation reactions catalyzed by cytochrome p450 enzymes". Chemical Reviews. 104 (9): 3947–3980. doi:10.1021/cr020443g. PMID   15352783. S2CID   33927145.
  10. ↑ Poulos TL, Finzel BC, Howard AJ (June 1987). "High-resolution crystal structure of cytochrome P450cam". Journal of Molecular Biology. 195 (3): 687–700. doi:10.1016/0022-2836(87)90190-2. PMID   3656428.
  11. ↑ Sligar SG, Cinti DL, Gibson GG, Schenkman JB (October 1979). "Spin state control of the hepatic cytochrome P450 redox potential". Biochemical and Biophysical Research Communications. 90 (3): 925–932. doi:10.1016/0006-291X(79)91916-8. PMID   228675.
  12. 1 2 Rittle J, Green MT (November 2010). "Cytochrome P450 Compound I: Capture, Characterization, and C-H Bond Activation Kinetics". Science. 330 (6006): 933–937. Bibcode:2010Sci...330..933R. doi:10.1126/science.1193478. PMID   21071661. S2CID   206528205.
  13. 1 2 Ortiz de Montellano PR (2005). Cytochrome P450: structure, mechanism, and biochemistry (3rd ed.). New York: Kluwer Academic/Plenum Publishers. ISBN   978-0-306-48324-0.
  14. ↑ Huang X, Groves JT (March 2018). "Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins". Chemical Reviews. 118 (5): 2491–2553. doi:10.1021/acs.chemrev.7b00373. PMC   5855008 . PMID   29286645.
  15. ↑ Hopper CP, Zambrana PN, Goebel U, Wollborn J (June 2021). "A brief history of carbon monoxide and its therapeutic origins". Nitric Oxide. 111–112: 45–63. doi:10.1016/j.niox.2021.04.001. PMID   33838343. S2CID   233205099.
  16. ↑ Smith AT, Pazicni S, Marvin KA, Stevens DJ, Paulsen KM, Burstyn JN (April 2015). "Functional divergence of heme-thiolate proteins: a classification based on spectroscopic attributes". Chemical Reviews. 115 (7): 2532–2558. doi:10.1021/cr500056m. PMID   25763468.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.