Abstract
Aspects of cytochrome P450 (CYP) nomenclature are addressed. The rules for naming a P450 are outlined, though individuals should not name their own genes. The nomenclature is presented as a unifying principle to enhance communication across disciplines. Because of the historical nature of gene sequencing, sometimes names have to be changed, but this is kept to a bare minimum to avoid confusion in the literature. CYP names have now reached four digits owing to proliferation of CYP families in the fungi and lower eukaryotes. For example, CYP5034A1 is from Ustilago maydis. P450 sequence motifs are described that are useful in making global alignments. CYP clans are defined as clusters of CYP families. The clan names are useful in describing higher-order evolution of the gene superfamily. The nomenclature of orthologs and pseudogenes is also discussed.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Nebert, D. W., Adesnik, M., Coon, M. J., et al. (1987) The P450 gene superfamily: recommended nomenclature. DNA 6, 1–11.
Nelson, D. R. (1998) Metazoan cytochrome P450 evolution. Comp. Biochem. Physiol. Pt. C 121, 15–22.
Nelson D. R. (1999) Cytochrome P450 and the individuality of species. Arch. Biochem. Biophys. 369, 1–10.
Gilbert, L. I. (2004) Halloween genes encode P450 enzymes that mediate steroid hormone biosynthesis in Drosophila melanogaster. Mol. Cell. Endocrinol. 215, 1–10.
Niwa, R., Matsuda, T., Yoshiyama, T., et al. (2004) CYP306A1, a cytochrome P450 enzyme, is essential for ecdysteroid biosynthesis in the prothoracic glands of Bombyx and Drosophila. J. Biol. Chem. 279, 35,942–35,949.
Warren, J. T., Petryk, A., Marques, G., et al. (2004) Phantom encodes the 25-hydroxylase of Drosophila melanogaster and Bombyx mori: a P450 enzyme critical in ecdysone biosynthesis. Insect Biochem. Mol. Biol. 34, 991–1010.
Petryk, A., Warren, J. T., Marques, G., et al. (2003) Shade is the Drosophila P450 enzyme that mediates the hydroxylation of ecdysone to the steroid insect molting hormone 20-hydroxyecdysone. Proc. Natl. Acad. Sci. USA 100, 13,773–13,778.
Nelson, D. R., Schuler, M. A., Paquette, S. M., Werck-Reichhart, D., and Bak, S. (2004) Comparative genomics of Oryza sativa and Arabidopsis thaliana: analysis of 727 Cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiol. 135, 756–772.
Eggertsen, G., Olin, M., Andersson, U., et al. (1996) Molecular cloning and expression of rabbit sterol 12alpha-hydroxylase. J. Biol. Chem. 271, 32,269–32,275.
Matsunaga, I., Yamada, A., Lee, D. S., et al. (2002) Enzymatic reaction of hydrogen peroxide-dependent peroxygenase cytochrome P450s: kinetic deuterium isotope effects and analyses by resonance Raman spectroscopy. Biochemistry 41, 1886–1892.
Peterson, J. A. and Graham-Lorence, S. E. (1995) Bacterial P450s: structural similarities and functional differences, in Cytochrome P450: Structure, Mechanism and Biochemistry, 2nd ed. (Ortiz de Montellano, P. R., ed.), Plenum, New York, pp. 151–180.
Nelson, D. R. (2004) Frankenstein genes, or the Mad Magazine version of the human pseudogenome. Hum. Genomics 1, 310–316.
Nelson, D. R., Zeldin, D. C., Hoffman, S. M. G., Maltais, L., Wain, H., and Nebert, D. W. (2004) Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes including nomenclature recommendations for genes, pseudogenes, and alternative-splice variants. Pharmacogenetics 14, 1–18.
Nelson, D. R. (2003) Comparison of P450s from human and fugu: 420 million years of yertebrate P450 evolution. Arch. Biochem. Biophys. 409, 18–24.
Nebert, D. W., Anastassios, N. Vasiliou, V., and Nelson, D. R. (2004) Cyclophilin nomenclature problems, or, “A Visit from the Sequence Police.” Hum. Genomics 1, 381–388.
Romano, P. G., Horton, P., and Gray, J. E. (2004) The Arabidopsis cyclophilin gene family. Plant Physiol. 134, 1268–1282.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc.
About this protocol
Cite this protocol
Nelson, D.R. (2006). Cytochrome P450 Nomenclature, 2004. In: Phillips, I.R., Shephard, E.A. (eds) Cytochrome P450 Protocols. Methods in Molecular Biology, vol 320. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-998-2:1
Download citation
DOI: https://doi.org/10.1385/1-59259-998-2:1
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-58829-441-8
Online ISBN: 978-1-59259-998-1
eBook Packages: Springer Protocols