Cytochromes P450 (P450s or CYPs) are a superfamily of enzymes containing heme as a cofactor that mostly, but not exclusively, function as monooxygenases. However, they are not omnipresent; for example, they have not been found in Escherichia coli. In mammals, these enzymes oxidize steroids, fatty acids, xenobiotics, and participate in many biosyntheses.

The 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 ) and allele names (CYP Allele Nomenclature Committee). These similarity-based groupings are frequently recovered in phylogenetic analyses and members generally share features in their catalytic activities. Sometimes the suggested similarity thresholds do not exactly match what phylogenetic patterns show (e.g. a new member that is close to a family but only 39% identical), causing what is known as "family creep" as the similarity threshold is reduced, or the occasional split of families.

There is a universal nomenclature for the assignment of P450 family numbers across the taxonomic groups:

  • CYP6001–CYP6099: Fungal fusions of P450s with other enzymes, e.g. dioxygenases or peroxygenases or isomerases.
  • CYP71–99, CYP701–CYP999, ...: Plants (Archaeplastida)
  • CYP101–299, ... Bacteria

The taxonomic group blocks are defined for CYP1001–CYP69999 by stretching the taxonomic blocks defined for CYP101–999. For example, CYP3001–4999 and CYP30001–CYP49999 are allocated to animals. The reservations defined under these groups are not stretched. Several databases are available for the tracking of defined P450 family numbers, subfamily letters, and ortholog group numbers, with the intention that not only there is no ambiguity in what each family-subfamily prefix means, but also that identically-named genes across different species are orthologous to each other. , the most complete database is the P450 Atlas (version 1.3.0) covering 11068 families, 26037 subfamilies, 79577 ortholog groups and 164068 example sequences of ortholog groups.

Comparison between many P450 enzymes of different families give rise to the concept of clans, evolutionary grouping of families. The exact similarity cut-off is poorly defined, but it is generally understood that it should derive from a few first-diverging nodes of a phylogenetic tree. Some clans only have one family while others are highly diversified with many families within (e.g. CYP71-clan and CYP85-clan). Tracking the emergence of clans and families across many taxonomic groups paints a vivid picture of the evolution of metabolic capabilities.

By electron transfer system

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

  • CPR-P450 systems combine a cytochrome P450 reductase (CPR) and a P450 domain.
  • Microsomal P450 systems in which electrons are transferred from NADPH via a CPR (variously CPR, POR, or CYPOR).
  • Also found in bacteria such as the P450meg (CYP106A2) from Bacillus megaterium.
  • Fr/Fd/P450 systems which employ a ferredoxin reductase and a ferredoxin to transfer electrons to P450. A representative is the plant plastid P450cam (CYP101A1) system from the CAM operon for camphor-related substrates. 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, and changing the state of the heme iron from low-spin to high-spin.
  2. Substrate binding induces electron transfer from NAD(P)H via cytochrome P450 reductase or another associated reductase, 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 b<sub>5</sub>, reducing the Fe-O<sub>2</sub> 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, 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

Spectroscopy

Binding of substrate is reflected in the spectral properties of the enzyme, with an increase in absorbance at 390&nbsp;nm and a decrease at 420&nbsp;nm. This can be measured by difference spectroscopies and is referred to as the "type&nbsp;I" difference spectrum (see inset graph in figure). Some substrates cause an opposite change in spectral properties, a "reverse type&nbsp;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&nbsp;II difference spectrum, with a maximum at 430&nbsp;nm and a minimum at 390&nbsp;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

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&nbsp;nm. However, the interruptive and inhibitory effects of CO varies upon different CYPs such that the CYP3A family is relatively less affected.

Binding site

[[File:Cytochrome P450 Binding Site.png|thumb|The conserved sequence of cytochrome P450 is highlighted, depicting how specific amino acid residues are essential for binding to a heme. In cytochrome p450 as seen in Streptomyces antibioticus (PDB code 4XE3), Phe349, Gly352, Ala353, Cys356, and Gly358 represent the conserved domain.]]

The heme in cytochrome P450 binds to a conserved sequence: <code>FxxGxRxCxG</code>, where "x" denotes some variant amino acid. The cysteine (C) binds Fe and arginine (R), forming strong electrostatic interactions with negatively charged side chains of the heme. The glycine (G) residues within the conserved sequence are essential, as their small structure enables surrounding alpha helices to remain in place without interacting with a variant amino acid. Additional conserved motifs are:

  • <code>ExxR</code> (K-helix)

See also

  • Cytochrome P450 oxidoreductase deficiency
  • Cytochrome P450 engineering
  • Pharmacogenomics

Further reading

References