CYP1A2

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Cytochrome P450, family 1, subfamily A, polypeptide 2
Image:PBB Protein CYP1A2 image.jpg
PDB rendering based on 2hi4.
Available structures:
For the file format that describes the 3D structures of molecules found in the Protein Data Bank, see Protein Data Bank (file format).

The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. These data, typically obtained by X-ray crystallography or NMR spectroscopy, are submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free.

History

Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB).

The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.

The PDB is a key resource in structural biology and is critical to more recent work in structural genomics.

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Growth

When the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off.

The growth rate of the PDB has been the subject of fairly extensive analysis.

Contents

As of 26 September, 2006, the database contained 39,051 released atomic coordinate entries (or "structures"), 35,767 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose.

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Statistics

As of 11 September, 2007, the "PDB Holdings List" at RCSB reported the following statistics:

Proteins Nucleic Acids Protein/NA complexes Other Total
X-ray diffraction 36223 983 1684 24 38914
NMR 5665 781 134 7 6587
Electron microscopy 105 10 38 0 153
Other 80 4 4 2 90
Total 42073 1778 1860 33 45744

Note that theoretical models are no longer accepted in the PDB.

22461 structures in the PDB have a structure factor file. 3138 structures in the PDB have an NMR restraint file.

The current breakdown of holdings is updated weekly.

File format

Through the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards.

This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects;

The MMDB uses ASN.1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i.e., a common dictionary), it is not possible to draw comparisons.

Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs.

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Viewing the data

The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software.

References

Printed

  • H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980 PMID 14634627.
  • H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID 10592235
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. PMID 875032.
  • E.F. Meyer “The First Years of the Protein Data Bank“, Protein Science 6:1591-1597 (1997)
  • Sussman, JL, Lin, D, Jiang, J, Manning, NO, Prilusky, J, Ritter, O & Abola, EE. Protein data bank (PDB): a database of 3D structural information of biological macromolecules. Acta Cryst 1998; D54:1078-1084. PMID 10089483.

Online

Other external links

Links to enzyme database data

  • [1] The best mapping is provided by Kim Henrick's group at EBI as part of the MSD SIFTS initiative.
  • [2] PDB provide a mapping on their beta site, but it is at the whole PDB level not chain level.
  • [3] Search at BRENDA enzyme database portal.
  • [4] PDBSProtEC:

Molecular graphic visualisation tools

Identifiers
Symbol(s) CYP1A2; CP12; P3-450; P450(PA)
External IDs OMIM: 124060 MGI: 88589 Homologene: 68082
RNA expression pattern

Image:PBB GE CYP1A2 207609 s at tn.png

Image:PBB GE CYP1A2 207608 x at tn.png

More reference expression data

Orthologs
Human Mouse
Entrez 1544 13077
Ensembl ENSG00000140505 ENSMUSG00000032310
Uniprot P05177 P00186
Refseq NM_000761 (mRNA)
NP_000752 (protein) 		NM_009993 (mRNA)
NP_034123 (protein)
Location Chr 15: 72.83 - 72.84 Mb Chr 9: 57.48 - 57.48 Mb
Pubmed search [5] [6]

Cytochrome P450 1A2 (abbreviated CYP1A2), a member of the cytochrome P450 mixed-function oxidase system, is involved in the metabolism of xenobiotics in the body.

Expression of CYP1A2 appears to be induced by various dietary constituents.[1]


CYP1A2 Ligands

Table of selected substrates, inducers and inhibitors of CYP1A21

Substrates Inhibitors Inducers
Often mentioned [1]:

Other:

Strong [1]:

unspecified:

Often mentioned[1]:

Other:

References

  • Meijerman I, Beijnen J, Schellens J. "Herb-drug interactions in oncology: focus on mechanisms of induction". Oncologist 11 (7): 742-52. PMID 16880233.

Further reading

  • Smith G, Stubbins MJ, Harries LW, Wolf CR (1999). "Molecular genetics of the human cytochrome P450 monooxygenase superfamily.". Xenobiotica 28 (12): 1129-65. PMID 9890157.
  • Landi MT, Sinha R, Lang NP, Kadlubar FF (1999). "Human cytochrome P4501A2.". IARC Sci. Publ. (148): 173-95. PMID 10493258.
  • Nelson DR, Zeldin DC, Hoffman SM, et al. (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): 1-18. PMID 15128046.
  • Ikeya K, Jaiswal AK, Owens RA, et al. (1990). "Human CYP1A2: sequence, gene structure, comparison with the mouse and rat orthologous gene, and differences in liver 1A2 mRNA expression.". Mol. Endocrinol. 3 (9): 1399-408. PMID 2575218.
  • Butler MA, Iwasaki M, Guengerich FP, Kadlubar FF (1989). "Human cytochrome P-450PA (P-450IA2), the phenacetin O-deethylase, is primarily responsible for the hepatic 3-demethylation of caffeine and N-oxidation of carcinogenic arylamines.". Proc. Natl. Acad. Sci. U.S.A. 86 (20): 7696-700. PMID 2813353.
  • Quattrochi LC, Okino ST, Pendurthi UR, Tukey RH (1986). "Cloning and isolation of human cytochrome P-450 cDNAs homologous to dioxin-inducible rabbit mRNAs encoding P-450 4 and P-450 6.". DNA 4 (5): 395-400. PMID 3000715.
  • Quattrochi LC, Pendurthi UR, Okino ST, et al. (1986). "Human cytochrome P-450 4 mRNA and gene: part of a multigene family that contains Alu sequences in its mRNA.". Proc. Natl. Acad. Sci. U.S.A. 83 (18): 6731-5. PMID 3462722.
  • Wrighton SA, Campanile C, Thomas PE, et al. (1986). "Identification of a human liver cytochrome P-450 homologous to the major isosafrole-inducible cytochrome P-450 in the rat.". Mol. Pharmacol. 29 (4): 405-10. PMID 3517618.
  • Jaiswal AK, Nebert DW, McBride OW, Gonzalez FJ (1988). "Human P(3)450: cDNA and complete protein sequence, repetitive Alu sequences in the 3' nontranslated region, and localization of gene to chromosome 15.". J. Exp. Pathol. 3 (1): 1-17. PMID 3681487.
  • Jaiswal AK, Nebert DW, Gonzalez FJ (1986). "Human P3(450): cDNA and complete amino acid sequence.". Nucleic Acids Res. 14 (16): 6773-4. PMID 3755823.
  • Eugster HP, Probst M, Würgler FE, Sengstag C (1993). "Caffeine, estradiol, and progesterone interact with human CYP1A1 and CYP1A2. Evidence from cDNA-directed expression in Saccharomyces cerevisiae.". Drug Metab. Dispos. 21 (1): 43-9. PMID 8095225.
  • Schweikl H, Taylor JA, Kitareewan S, et al. (1994). "Expression of CYP1A1 and CYP1A2 genes in human liver.". Pharmacogenetics 3 (5): 239-49. PMID 8287062.
  • Yamazaki H, Inoue K, Mimura M, et al. (1996). "7-Ethoxycoumarin O-deethylation catalyzed by cytochromes P450 1A2 and 2E1 in human liver microsomes.". Biochem. Pharmacol. 51 (3): 313-9. PMID 8573198.
  • Hakkola J, Raunio H, Purkunen R, et al. (1996). "Detection of cytochrome P450 gene expression in human placenta in first trimester of pregnancy.". Biochem. Pharmacol. 52 (2): 379-83. PMID 8694864.
  • Guengerich FP, Johnson WW (1998). "Kinetics of ferric cytochrome P450 reduction by NADPH-cytochrome P450 reductase: rapid reduction in the absence of substrate and variations among cytochrome P450 systems.". Biochemistry 36 (48): 14741-50. doi:10.1021/bi9719399. PMID 9398194.
  • Wacke R, Kirchner A, Prall F, et al. (1998). "Up-regulation of cytochrome P450 1A2, 2C9, and 2E1 in chronic pancreatitis.". Pancreas 16 (4): 521-8. PMID 9598815.
  • Macé K, Bowman ED, Vautravers P, et al. (1998). "Characterisation of xenobiotic-metabolising enzyme expression in human bronchial mucosa and peripheral lung tissues.". Eur. J. Cancer 34 (6): 914-20. PMID 9797707.
  • Huang JD, Guo WC, Lai MD, et al. (1999). "Detection of a novel cytochrome P-450 1A2 polymorphism (F21L) in Chinese.". Drug Metab. Dispos. 27 (1): 98-101. PMID 9884316.
  • Tatemichi M, Nomura S, Ogura T, et al. (1999). "Mutagenic activation of environmental carcinogens by microsomes of gastric mucosa with intestinal metaplasia.". Cancer Res. 59 (16): 3893-8. PMID 10463577.

See also

v • d • e
Cytochromes, oxygenases: cytochrome P450 (EC 1.14)
CYP1A1, A2, B1
CYP2A6, A7, A13, B6, C8, C9, C18, C19, D6, E1, F1, J2, R1, S1, U1, W1
CYP3A4, A5, A7, A43
CYP4A11, A22, B1, F2, F3, F8, F11, F12, F22, V2, X1, Z1
CYP5-20CYP5 (A1) - CYP7 (A1, B1) - CYP8 (A1, B1) - CYP11 (A1, B1, B2) - CYP17 (A1) - CYP19 (A1) - CYP20 (A1)
CYP21-51CYP21 (A2) - CYP24 (A1) - CYP26 (A1, B1, C1) - CYP27 (A1, B1, C1) - CYP39 (A1) - CYP46 (A1) - CYP51 (A1)


Acknowledgement and Attribution Regarding Sources of Content

Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). Differential Diagnoses are drawn from clinicians as well as an amalgamation of 3 sources: 1.The Disease Database; 2. Kahan, Scott, Smith, Ellen G. In A Page: Signs and Symptoms. Malden, Massachusetts: Blackwell Publishing, 2004:3; 3. Sailer, Christian, Wasner, Susanne. Differential Diagnosis Pocket. Hermosa Beach, CA: Borm Bruckmeir Publishing LLC, 2002:7 .

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