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CYP4B1 (cytochrome P450, family 4, subfamily B, polypeptide 1)

Written2012-02Edward J Kelly, Vladimir Yarov-Yarovoy, Allan E Rettie
Department of Pharmaceutics, University of Washington, Seattle, USA (EJK); Department of Physiology, Membrane Biology, Department of Biochemistry, Molecular Medicine, School of Medicine, University of California, Davis, USA (VYY); Department of Medicinal Chemistry, University of Washington, Seattle, USA (AER)

(Note : for Links provided by Atlas : click)

Identity

Alias_namescytochrome P450, subfamily IVB, polypeptide 1
cytochrome P450, family 4, subfamily B, polypeptide 1
Other aliasCYPIVB1
P-450HP
HGNC (Hugo) CYP4B1
LocusID (NCBI) 1580
Atlas_Id 40253
Location 1p33  [Link to chromosome band 1p33]
Location_base_pair Starts at 46798998 and ends at 46819349 bp from pter ( according to hg19-Feb_2009)  [Mapping CYP4B1.png]
Fusion genes
(updated 2016)
CYP4B1 (1p33) / CYP4B1 (1p33)CYP4B1 (1p33) / NEDD4L (18q21.31)

DNA/RNA

 
  Figure 1. Localization of the CYP4B1 locus to chromosome 1p33 and sites (exons 5, 8 and 9) of polymorphic variants that describe the 7 allelic variants of CYP4B1 (see table 1 for details).
Description The CYP4B1 gene has 12 exons resulting in an open reading frame of 1533 bp (isoform 1). The CYP4B1 locus is depicted in figure 1 (NCBI).
Transcription Two major transcripts are known to derive from alternative splicing (NM_000779.3, NM_001099772.1). Isoform 1 encodes a 511 amino acid protein, while isoform 2 encodes a 512 amino acid protein with a Ser206 insertion. It should be noted that this is a complicated locus with many other possibilities for alternative splicing.
Pseudogene No pseudogene is known for CYP4B1.

Protein

Note CYP4B1 belongs to the mammalian CYP4 enzyme family that also includes CYP4A, 4F and the recently discovered CYP 4V, 4X and 4Z sub-families (Rettie and Kelly, 2008). P450 enzymes usually function as monooxygenases in that they incorporate one atom of molecular oxygen into their substrates and reduce the other to water. CYP4 enzymes typically catalyze fatty acid ω-hydroxylase reactions.
Description Structurally, P450 enzymes all share a similar fold featuring a β-sheet rich N-terminus and an α-helix rich C-terminus. The hydrophobic N-terminus of eukaryotic P450s functions as membrane anchor, whereas the C-terminal region houses the cysteinyl heme (iron protoporphyrin IX) cofactor that binds and activates molecular oxygen. Many CYP4 enzymes, including CYP4B1, possess a unique post-translational modification at the heme active center, wherein a conserved glutamate residue in the core I-helix forms a covalent, ester linkage at the C-5 methyl group of the heme (Henne et al., 2001). The function of the unusual modification has not been established, although it may serve to rigidify the enzyme's active site and modulate the substrate selectivity of CYP4B1. The CYP4B1 enzyme is highly conserved across species - see figure 2 below that also highlights the position of the cysteinyl ligand and the I-helix glutamate.
 
  Figure 2. Multiple sequence alignment of vertebrate CYP4B proteins. The covalently heme-linked glutamate residue is indicated in bold italics and the heme-coordinating cysteinyl ligand depicted in bold underline. The Pro>Ser substitution at position 427 in human CYP4B1 is depicted in italics. Alignments determined using the ClustalW2 multiple sequence alignment program available online at EMBL-EBI.
Expression CYP4B1 mRNA and/or protein are found typically at the highest levels in lung and airway tissue. Liver levels of the enzyme are usually much lower, but inducible by phenobarbital. Expression of the enzyme in mouse kidney is regulated by androgens. CYP4B1 is highly expressed in several cancer types, including colon, adrenal gland, lung and gastric cancers.
Localisation CYP4B1 is located in the ER membrane, although one report suggests that the rat enzyme may be a secreted protein in respiratory mucosa (Genter et al., 2006).
Function CYP4B1 is functionally related to the larger mammalian CYP4 family through maintenance of ω-hydroxylase activity towards fatty acids and alkyl hydrocarbons, which may be reflective of its endogenous role. Indeed, a strong link has been made between CYP4B1 levels, 12-HETrE production, and angiogenic activity in the rabbit cornea (Seta et al., 2007). Additionally, CYP4B1 has the capacity to metabolize a diverse array of xenobiotic pro-toxins, including valproic acid, 3-methylindole, 4-ipomeanol, and numerous aromatic amines. While these xenobiotics have little in common structurally or chemically, their metabolism by CYP4B1 leads to reactive metabolites that may cause tissue-specific toxicities in several experimental animals. The bioactivation capabilities of rabbit CYP4B1 have attracted attention in the cancer community and formed the basis of an experimental therapeutic strategy involving prodrug-activation by the CYP4B1 transgene (Rainov et al., 1998). The metabolic capabilities of human CYP4B1 are much less clear due to difficulties in heterologous expression of active enzyme and/or the existence of alternatively spliced products. Note that human CYP4B1 also uniquely possesses a Ser instead of a Pro residue at amino acid position 427 (see figure 3) - a sequence variation that has been suggested to result in a functionally defective enzyme (Zheng et al., 1998).
 
  Figure 3. Homology model of CYP4B1 based on human P450 1A2 structure (Sansen et al., 2007), highlighting the location of the Pro>Ser substitution unique to the human isozyme. Structure shown in ribbon representation and colored by a rainbow scheme from N-terminus (blue) to C-terminus (red). S427 is shown in spacefilling representation and labeled. Heme shown in ball and stick representation.
Homology - CYP4B1 (Pan troglodytes)
- Cyp4b1 (Mus musculus)
- Cyp4b1 (Rattus norvegicus)
- CYP4B1 (Oryctolagus cuniculus)
- CYP4B1 (Bos Taurus)
- CYP4B1 (Canis lupus)
- CYP4B1 (Gallus gallus)
- CYP4B1 (Xenopus laevis)

Denoted as similar to CYP4B1:
- CYP4B2 (Capra hircus)
- cyp4t8 (Danio rerio)

Mutations

Note Seven alleles (CYP4B1*1-*7) are listed at http://www.cypalleles.ki.se/cyp4b1.htm and summarized in table 1 below. The CYP4B1*1 allele is described by a composition of the major alleles shown in table 1. CYP4B1*2 contains the haplotype of the 294 frameshift along with M331I, R340C and R375C. CYP4B1*7 is the same haplotype minus the R375C variant. CYP4B1*3/4/5 are described by the R173W, S322G and M331I polymorphisms, respectively. CYP4B1*6 is R173W in combination with V345I.

Nucleotide Change, cDNA positionProtein Coding Sequence ChangeHeterozygosity1
517C>TR173W0.28
881_882ΔAT294 frameshift (STOP)0.34
964A>GS322G0.02
993G>AM331I0.40
1018C>TR340C0.22
1033G>AV345IND
1123C>TR375C0.26
Table 1. CYP4B1 polymorphic variants including nucleotide changes and effect on protein coding sequences. 1 The values for heterozygosity of the minor alleles are taken from NCBI. ND: not determined.

Recent exome sequencing has revealed considerable additional polymorphism (>75 total SNPs) in the human CYP4B1 gene (search at Exome Variant Server).

Implicated in

Note
  
Entity Various cancers
Note CYP4B1 mRNA and/or protein are highly expressed in some cancer types. In particular Imaoka et al. demonstrated increased CYP4B1 in bladder tumor tissue at both the mRNA and protein level (Imaoka et al., 2000). This finding is also consistent with rodent studies demonstrating localization of CYP4B1 in mouse and rat bladder tissue (Imaoka et al., 1997; Imaoka et al., 2001). However, Czerwinski et al. observed down regulation of CYP4B1 mRNA in lung tumors relative to normal lung (Czerwinski et al., 1994). With breast cancer, there does not appear to be any difference in expression of CYP4B1 when comparing tumor tissue with surrounding healthy tissue, but these studies did not use disease-free subjects as a comparator (Iscan et al., 2001). Relatively high expression of constitutive CYP4B1 mRNA has been found in human urothelial cells (Roos et al., 2006). Peripheral blood mononuclear cell CYP4B1 mRNA expression correlated with human liver expression and therefore has been suggested as a surrogate marker for hepatic bioactivation of environmental pro-toxins (Furukawa et al., 2004). An increased risk of bladder cancer (OR of 1.03-2.95) has been reported in Japanese patients carrying the CYP4B1*2 allele (Sasaki et al., 2008). One potential explanation could be that CYP4B1 is known to play a role in aromatic amine bioactivation (Windmill et al., 1997) and these compounds are known bladder carcinogens and present in cooked meats (Jägerstad and Skog, 2005) and cigarette smoke (Smith et al., 1997), among other sources. However, no association was found between lung cancer risk and CYP4B1*1-*7 polymorphisms in Japanese (Tamaki et al., 2011).
  
  
Entity Angiogenesis
Note Studies conducted in a rabbit model of corneal wound healing have implicated that CYP4B1 may play a role in production of inflammatory eicosanoids and corneal neovascularization (Mastyugin et al., 2001). These observations are corroborated by findings in mice, whereby heme oxygenase-I induction attenuates corneal inflammation and is associated with a lack of CYP4B1 induction (and eicosanoid production) (Patil et al., 2008). Conversely, retinoic acid (RA) has been shown to increase CYP4B1 gene expression in ocular organ cultures, resulting in increased metabolism of arachidonic acid to 12-HETE and 12-HETrE (Ashkar et al., 2004). These effects were shown to be mediated, at least in part, by transcriptional regulation of the rabbit CYP4B1 promoter, which contains several RAR/RXR binding motifs (Ashkar et al., 2004). While RA is typically associated with corneal wound healing, the induction of CYP4B1 by RA suggests it may also have a pro-inflammatory role in wound healing. This is supported by the observation that systemic treatment with 13-cis-retinoic acid (Accutane™) for cystic acne is associated with conjunctivitis, eyelid inflammation and keratitis, along with other ocular effects (Lebowitz and Berson, 1988). Further evidence that CYP4B1 is important in ocular inflammation, eicosanoid production and neovascularization is shown in a study by Seta et al., using in vivo siRNA targeting of CYP4B1 in a rabbit model of corneal wound healing. It was found that down-regulation of CYP4B1 inhibited production of 12- HETrE and VEGF in addition to decreasing neovascularization (Seta et al., 2007).
  
  
Entity Colitis
Note Several recent studies have implicated a potential role for CYP4B1 in inflammatory bowel disease (IBD). In a mouse model of dextran sodium sulfate (DSS)-induced colitis, Ye et al. found that caffeic acid treatment decreased disease severity and this was associated with increased expression of Cyp4b1 in affected tissues (Ye et al., 2009). In a subsequent study looking at the role of caffeic acid bioavailability in this model, they found that mice treated with DSS alone had lower colonic Cyp4b1 expression when compared to DSS plus caffeic acid treated mice (Ye et al., 2011). In a different mouse model of IBD, Liu et al. also found evidence that Cyp4b1 gene expression is altered in this disease state (Liu et al., 2009). It was found that IBD induced by infection with Helicobacter bilis resulted in changes in mucosal gene expression patterns. Using microarray analysis, it was found that H. bilis infection resulted in decreased expression of Cyp4b1. These authors also examined mice with IBD induced by DSS and, akin to Liu et al., found decreased expression of Cyp4b1 in diseased tissue. These findings suggest an anti-inflammatory role for CYP4B1 in IBD, but these preclinical studies must be weighed against what is known about gastrointestinal expression of CYP4B1 and human IBD. While rodents and rabbits and other species are known to expression CYP4B1 in the gut, there are species-specific differences, with humans expressing little CYP4B1 in this tissue (McKinnon et al., 1994). Whether the CYP4B1 gene plays any role in IBD is unclear, particularly in light of the functionality of the Pro427Ser human protein (Zheng et al., 1998). Finally, in considering risk of developing IBD, a genome wide association study by The Wellcome Trust examining 2000 cases of Crohn's with 3000 controls, found no significant association between CYP4B1 genetic variants and disease incidence (Wellcome Trust Case Control Consortium, 2007).
  

Bibliography

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Localization of CYP4B1 in the rat nasal cavity and analysis of CYPs as secreted proteins.
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Covalent linkage of prosthetic heme to CYP4 family P450 enzymes.
Henne KR, Kunze KL, Zheng YM, Christmas P, Soberman RJ, Rettie AE.
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Androgen regulation of CYP4B1 responsible for mutagenic activation of bladder carcinogens in the rat bladder: detection of CYP4B1 mRNA by competitive reverse transcription-polymerase chain reaction.
Imaoka S, Yoneda Y, Sugimoto T, Ikemoto S, Hiroi T, Yamamoto K, Nakatani T, Funae Y.
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The expression of cytochrome P450 enzymes in human breast tumours and normal breast tissue.
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Mucosal gene expression profiles following the colonization of immunocompetent defined-flora C3H mice with Helicobacter bilis: a prelude to typhlocolitis.
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Corneal epithelial VEGF and cytochrome P450 4B1 expression in a rabbit model of closed eye contact lens wear.
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Heme oxygenase-1 induction attenuates corneal inflammation and accelerates wound healing after epithelial injury.
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New prodrug activation gene therapy for cancer using cytochrome P450 4B1 and 2-aminoanthracene/4-ipomeanol.
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The CYP4 Family
Rettie A E, Kelly EJ.
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Possible relationship between the risk of Japanese bladder cancer cases and the CYP4B1 genotype.
Sasaki T, Horikawa M, Orikasa K, Sato M, Arai Y, Mitachi Y, Mizugaki M, Ishikawa M, Hiratsuka M.
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PMID 18713828
 
Inhibition of VEGF expression and corneal neovascularization by siRNA targeting cytochrome P450 4B1.
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Increased CYP4B1 mRNA is associated with the inhibition of dextran sulfate sodium-induced colitis by caffeic acid in mice.
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Citation

This paper should be referenced as such :
Kelly, EJ ; Yarov-Yarovoy, V ; Rettie, AE
CYP4B1 (cytochrome P450, family 4, subfamily B, polypeptide 1)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(7):453-458.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CYP4B1ID40253ch1p33.html


External links

Nomenclature
HGNC (Hugo)CYP4B1   2644
Cards
AtlasCYP4B1ID40253ch1p33
Entrez_Gene (NCBI)CYP4B1  1580  cytochrome P450 family 4 subfamily B member 1
AliasesCYPIVB1; P-450HP
GeneCards (Weizmann)CYP4B1
Ensembl hg19 (Hinxton)ENSG00000142973 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000142973 [Gene_View]  chr1:46798998-46819349 [Contig_View]  CYP4B1 [Vega]
ICGC DataPortalENSG00000142973
TCGA cBioPortalCYP4B1
AceView (NCBI)CYP4B1
Genatlas (Paris)CYP4B1
WikiGenes1580
SOURCE (Princeton)CYP4B1
Genetics Home Reference (NIH)CYP4B1
Genomic and cartography
GoldenPath hg38 (UCSC)CYP4B1  -     chr1:46798998-46819349 +  1p33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CYP4B1  -     1p33   [Description]    (hg19-Feb_2009)
EnsemblCYP4B1 - 1p33 [CytoView hg19]  CYP4B1 - 1p33 [CytoView hg38]
Mapping of homologs : NCBICYP4B1 [Mapview hg19]  CYP4B1 [Mapview hg38]
OMIM124075   
Gene and transcription
Genbank (Entrez)AF491285 AK225576 AK225578 AK300921 AK300941
RefSeq transcript (Entrez)NM_000779 NM_001099772 NM_001319161 NM_001319162 NM_001319163
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CYP4B1
Cluster EST : UnigeneHs.436317 [ NCBI ]
CGAP (NCI)Hs.436317
Alternative Splicing GalleryENSG00000142973
Gene ExpressionCYP4B1 [ NCBI-GEO ]   CYP4B1 [ EBI - ARRAY_EXPRESS ]   CYP4B1 [ SEEK ]   CYP4B1 [ MEM ]
Gene Expression Viewer (FireBrowse)CYP4B1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1580
GTEX Portal (Tissue expression)CYP4B1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP13584   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP13584  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP13584
Splice isoforms : SwissVarP13584
Catalytic activity : Enzyme1.14.14.1 [ Enzyme-Expasy ]   1.14.14.11.14.14.1 [ IntEnz-EBI ]   1.14.14.1 [ BRENDA ]   1.14.14.1 [ KEGG ]   
PhosPhoSitePlusP13584
Domaine pattern : Prosite (Expaxy)CYTOCHROME_P450 (PS00086)   
Domains : Interpro (EBI)Cyt_P450    Cyt_P450_CS    Cyt_P450_E_grp-I   
Domain families : Pfam (Sanger)p450 (PF00067)   
Domain families : Pfam (NCBI)pfam00067   
Conserved Domain (NCBI)CYP4B1
DMDM Disease mutations1580
Blocks (Seattle)CYP4B1
SuperfamilyP13584
Human Protein AtlasENSG00000142973
Peptide AtlasP13584
HPRD00491
IPIIPI00465029   IPI00644258   IPI00909347   IPI00643879   IPI00984651   IPI00984021   IPI01014885   IPI01015302   IPI01010561   IPI01014466   
Protein Interaction databases
DIP (DOE-UCLA)P13584
IntAct (EBI)P13584
FunCoupENSG00000142973
BioGRIDCYP4B1
STRING (EMBL)CYP4B1
ZODIACCYP4B1
Ontologies - Pathways
QuickGOP13584
Ontology : AmiGOiron ion binding  endoplasmic reticulum membrane  drug binding  toxic substance binding  fluorene oxygenase activity  biphenyl metabolic process  fluorene metabolic process  oxygen binding  heme binding  organelle membrane  exogenous drug catabolic process  oxidation-reduction process  aromatase activity  
Ontology : EGO-EBIiron ion binding  endoplasmic reticulum membrane  drug binding  toxic substance binding  fluorene oxygenase activity  biphenyl metabolic process  fluorene metabolic process  oxygen binding  heme binding  organelle membrane  exogenous drug catabolic process  oxidation-reduction process  aromatase activity  
Pathways : BIOCARTANuclear Receptors in Lipid Metabolism and Toxicity [Genes]   
REACTOMEP13584 [protein]
REACTOME PathwaysR-HSA-2142691 [pathway]   
NDEx NetworkCYP4B1
Atlas of Cancer Signalling NetworkCYP4B1
Wikipedia pathwaysCYP4B1
Orthology - Evolution
OrthoDB1580
GeneTree (enSembl)ENSG00000142973
Phylogenetic Trees/Animal Genes : TreeFamCYP4B1
HOVERGENP13584
HOGENOMP13584
Homologs : HomoloGeneCYP4B1
Homology/Alignments : Family Browser (UCSC)CYP4B1
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCYP4B1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CYP4B1
dbVarCYP4B1
ClinVarCYP4B1
1000_GenomesCYP4B1 
Exome Variant ServerCYP4B1
ExAC (Exome Aggregation Consortium)CYP4B1 (select the gene name)
Genetic variants : HAPMAP1580
Genomic Variants (DGV)CYP4B1 [DGVbeta]
DECIPHERCYP4B1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCYP4B1 
Mutations
ICGC Data PortalCYP4B1 
TCGA Data PortalCYP4B1 
Broad Tumor PortalCYP4B1
OASIS PortalCYP4B1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCYP4B1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCYP4B1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CYP4B1
DgiDB (Drug Gene Interaction Database)CYP4B1
DoCM (Curated mutations)CYP4B1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CYP4B1 (select a term)
intoGenCYP4B1
NCG5 (London)CYP4B1
Cancer3DCYP4B1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM124075   
Orphanet
MedgenCYP4B1
Genetic Testing Registry CYP4B1
NextProtP13584 [Medical]
TSGene1580
GENETestsCYP4B1
Target ValidationCYP4B1
Huge Navigator CYP4B1 [HugePedia]
snp3D : Map Gene to Disease1580
BioCentury BCIQCYP4B1
ClinGenCYP4B1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1580
Chemical/Pharm GKB GenePA27119
Clinical trialCYP4B1
Miscellaneous
canSAR (ICR)CYP4B1 (select the gene name)
Probes
Litterature
PubMed37 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCYP4B1
EVEXCYP4B1
GoPubMedCYP4B1
iHOPCYP4B1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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