Vitamin D (calciferol) metabolism (Homo sapiens)

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74, 6, 17, 298, 10, 16, 22-2531927627271, 13, 3132275, 119, 18927, 286714TARGET CELLSKINendoplasmic reticulum lumenKIDNEYmitochondrial matrixcytosolcytosolendoplasmic reticulum lumenmitochondrial intermembrane spacecytosolLIVERnucleoplasmcytosollysosomal lumenO225(OH)D SUMO2-VDR25(OH)D PIAS4CYP24A1H+VD3 LGMNH2OVDR 25(OH)DUBE2I-G93-SUMO2 GC 25(OH)DCUBN 25(OH)D VD3O2CUBN:GC:25(OH)DNADPHSUMO2-C93-UBE2I NADP+SUMO2:UBE2ICUBN:GC:25(OH)DCUBN GC 25(OH)DVD31,25(OH)2DGC GC GC:25(OH)DCUBN:GC:25(OH)DNADPHLRP2CYP2R1CUBN 7-dehydroCHOLGC1,25(OH)2DH+H2OCUBN NADPHCYP27B1(?-508)UBE2I25(OH)DCholesterolbiosynthesisNADP+VD325(OH)D H2OGCCUBNVDRH+GC:VD3O2CTA1,25(OH)2D:VDRCUBNCUBN:25(OH)D1,25(OH)2D VD325(OH)D NADP+GC 26, 30192, 12, 15, 20, 21


Description

Vitamin D3 (VD3, cholecalciferol) is a steroid hormone that principally plays roles in regulating intestinal calcium absorption and in bone metabolism. It is obtained from the diet and produced in the skin by photolysis of 7-dehydrocholesterol and released into the bloodstream. Very few foods (eg. oily fish, mushrooms exposed to sunlight and cod liver oil) are natural sources of vitamin D. A small number of countries in the world artificially fortify a few foods with vitamin D. The metabolites of vitamin D are carried in the circulation bound to a plasma protein called vitamin D binding protein (GC) (for review see Delanghe et al. 2015, Chun 2012). Vitamin D undergoes two subsequent hydroxylations to form the active form of the vitamin, 1-alpha, 25-dihydroxyvitamin D (1,25(OH)2D). The first hydroxylation takes place in the liver followed by subsequent transport to the kidney where the second hydroxylation takes place. 1,25(OH)2D acts by binding to nuclear vitamin D receptors (Neme et al. 2017) and it has been estimated that upwards of 2000 genes are directly or indirectly regulated which are involved in calcium homeostasis, immune responses, cellular growth, differentiation and apoptosis (Hossein-nezhad et al. 2013, Hossein-nezhad & Holick 2013). Inactivation of 1,25(OH)2D occurs via C23/C24 oxidation catalysed by cytochrome CYP24A1 enzyme (Christakos et al. 2016). View original pathway at:Reactome.

Comments

Reactome-Converter 
Pathway is converted from Reactome ID: 196791
Reactome-version 
Reactome version: 66
Reactome Author 
Reactome Author: Jassal, Bijay

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Ontology Terms

 

Bibliography

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History

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CompareRevisionActionTimeUserComment
101322view11:21, 1 November 2018ReactomeTeamreactome version 66
100859view20:53, 31 October 2018ReactomeTeamreactome version 65
100400view19:27, 31 October 2018ReactomeTeamreactome version 64
99948view16:11, 31 October 2018ReactomeTeamreactome version 63
99504view14:44, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99150view12:41, 31 October 2018ReactomeTeamreactome version 62
93749view13:33, 16 August 2017ReactomeTeamreactome version 61
93268view11:18, 9 August 2017ReactomeTeamreactome version 61
86977view14:30, 15 July 2016MkutmonOntology Term : 'vitamin D metabolic pathway' added !
86345view09:15, 11 July 2016ReactomeTeamreactome version 56
86215view11:11, 7 July 2016ReactomeTeamNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
1,25(OH)2D MetaboliteCHEBI:17823 (ChEBI)
1,25(OH)2D:VDRComplexR-HSA-8963916 (Reactome)
1,25(OH)2DMetaboliteCHEBI:17823 (ChEBI)
25(OH)D MetaboliteCHEBI:17933 (ChEBI)
25(OH)DMetaboliteCHEBI:17933 (ChEBI)
7-dehydroCHOLMetaboliteCHEBI:17759 (ChEBI)
CTAMetaboliteCHEBI:47828 (ChEBI)
CUBN ProteinO60494 (Uniprot-TrEMBL)
CUBN:25(OH)DComplexR-HSA-8963847 (Reactome)
CUBN:GC:25(OH)DComplexR-HSA-350085 (Reactome)
CUBN:GC:25(OH)DComplexR-HSA-350092 (Reactome)
CUBN:GC:25(OH)DComplexR-HSA-350115 (Reactome)
CUBNProteinO60494 (Uniprot-TrEMBL)
CYP24A1ProteinQ07973 (Uniprot-TrEMBL)
CYP27B1(?-508)ProteinO15528 (Uniprot-TrEMBL) The start coordinate is not yet known
CYP2R1ProteinQ6VVX0 (Uniprot-TrEMBL)
Cholesterol biosynthesisPathwayR-HSA-191273 (Reactome) Cholesterol is synthesized de novo from acetyl CoA. The overall synthetic process is outlined in the attached illustration. Enzymes whose regulation plays a major role in determining the rate of cholesterol synthesis in the body are highlighted in red, and connections to other metabolic processes are indicated. The transformation of zymosterol into cholesterol can follow either of routes, one in which reduction of the double bond in the isooctyl side chain is the final step (cholesterol synthesis via desmosterol, also known as the Bloch pathway) and one in which this reduction is the first step (cholesterol biosynthesis via lathosterol, also known as the Kandutsch-Russell pathway). The former pathway is prominent in the liver and many other tissues while the latter is prominent in skin, where it may serve as the source of the 7-dehydrocholesterol that is the starting point for the synthesis of D vitamins. Defects in several of the enzymes involved in this process are associated with human disease and have provided useful insights into the regulatory roles of cholesterol and its synthetic intermediates in human development (Gaylor 2002; Herman 2003; Kandutsch & Russell 1960; Mitsche et al. 2015; Song et al. 2005).
GC ProteinP02774 (Uniprot-TrEMBL)
GC:25(OH)DComplexR-HSA-209892 (Reactome)
GC:VD3ComplexR-HSA-352339 (Reactome)
GCProteinP02774 (Uniprot-TrEMBL)
H+MetaboliteCHEBI:15378 (ChEBI)
H2OMetaboliteCHEBI:15377 (ChEBI)
LGMNProteinQ99538 (Uniprot-TrEMBL)
LRP2ProteinP98164 (Uniprot-TrEMBL)
NADP+MetaboliteCHEBI:18009 (ChEBI)
NADPHMetaboliteCHEBI:16474 (ChEBI)
O2MetaboliteCHEBI:15379 (ChEBI)
PIAS4ProteinQ8N2W9 (Uniprot-TrEMBL)
SUMO2-C93-UBE2I ProteinP63279 (Uniprot-TrEMBL)
SUMO2-VDRProteinP11473 (Uniprot-TrEMBL)
SUMO2:UBE2IComplexR-HSA-2993778 (Reactome)
UBE2I-G93-SUMO2 ProteinP61956 (Uniprot-TrEMBL)
UBE2IProteinP63279 (Uniprot-TrEMBL)
VD3 MetaboliteCHEBI:28940 (ChEBI)
VD3MetaboliteCHEBI:28940 (ChEBI)
VDR ProteinP11473 (Uniprot-TrEMBL)
VDRProteinP11473 (Uniprot-TrEMBL)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
1,25(OH)2D:VDRArrowR-HSA-8963915 (Reactome)
1,25(OH)2DArrowR-HSA-209868 (Reactome)
1,25(OH)2DArrowR-HSA-8963913 (Reactome)
1,25(OH)2DR-HSA-209765 (Reactome)
1,25(OH)2DR-HSA-8963913 (Reactome)
1,25(OH)2DR-HSA-8963915 (Reactome)
25(OH)DArrowR-HSA-209766 (Reactome)
25(OH)DArrowR-HSA-209845 (Reactome)
25(OH)DArrowR-HSA-6807242 (Reactome)
25(OH)DArrowR-HSA-8963864 (Reactome)
25(OH)DR-HSA-209766 (Reactome)
25(OH)DR-HSA-209868 (Reactome)
25(OH)DR-HSA-209944 (Reactome)
25(OH)DR-HSA-6807242 (Reactome)
7-dehydroCHOLR-HSA-209754 (Reactome)
CTAArrowR-HSA-209765 (Reactome)
CUBN:25(OH)DArrowR-HSA-350158 (Reactome)
CUBN:25(OH)DR-HSA-8963864 (Reactome)
CUBN:GC:25(OH)DArrowR-HSA-209760 (Reactome)
CUBN:GC:25(OH)DArrowR-HSA-350168 (Reactome)
CUBN:GC:25(OH)DArrowR-HSA-350186 (Reactome)
CUBN:GC:25(OH)DR-HSA-209760 (Reactome)
CUBN:GC:25(OH)DR-HSA-350158 (Reactome)
CUBN:GC:25(OH)DR-HSA-350168 (Reactome)
CUBNArrowR-HSA-8963864 (Reactome)
CUBNR-HSA-350186 (Reactome)
CYP24A1mim-catalysisR-HSA-209765 (Reactome)
CYP27B1(?-508)mim-catalysisR-HSA-209868 (Reactome)
CYP2R1mim-catalysisR-HSA-209845 (Reactome)
GC:25(OH)DArrowR-HSA-209944 (Reactome)
GC:25(OH)DR-HSA-350186 (Reactome)
GC:VD3ArrowR-HSA-209738 (Reactome)
GC:VD3R-HSA-8963851 (Reactome)
GCArrowR-HSA-8963851 (Reactome)
GCR-HSA-209738 (Reactome)
GCR-HSA-209944 (Reactome)
H+R-HSA-209765 (Reactome)
H+R-HSA-209845 (Reactome)
H+R-HSA-209868 (Reactome)
H2OArrowR-HSA-209765 (Reactome)
H2OArrowR-HSA-209845 (Reactome)
H2OArrowR-HSA-209868 (Reactome)
LGMNmim-catalysisR-HSA-350158 (Reactome)
LRP2mim-catalysisR-HSA-350168 (Reactome)
NADP+ArrowR-HSA-209765 (Reactome)
NADP+ArrowR-HSA-209845 (Reactome)
NADP+ArrowR-HSA-209868 (Reactome)
NADPHR-HSA-209765 (Reactome)
NADPHR-HSA-209845 (Reactome)
NADPHR-HSA-209868 (Reactome)
O2R-HSA-209765 (Reactome)
O2R-HSA-209845 (Reactome)
O2R-HSA-209868 (Reactome)
PIAS4mim-catalysisR-HSA-4546387 (Reactome)
R-HSA-209738 (Reactome) Vitamin D metabolites such as VD3 are lipophilic and must be transported in the circulation bound to plasma proteins. Vitamin D3 is transported to the liver bound to a plasma protein called vitamin D binding protein (GC aka DBP) (Verboven et al. 2002). GC is a 58 kDa circulating glycoprotein that transports vitamin D metabolites. The vast majority of vitamin D metabolites circulate bound to GC (85–90%), some bound to albumin (10–15%), with the remainder (<1%) circulating in the free form. GC has more than 1000-fold stronger binding affinity for vitamin D metabolites than albumin. Thus, the albumin-bound and free fractions of vitamin D metabolites are considered bioavailable (Denburg et al. 2016).
R-HSA-209754 (Reactome) The skin's exposure to UV rays from sunlight induces the photolytic cleavage of 7-dehydrocholesterol to previtamin D3. This is followed by thermal isomerization to form vitamin D3 (VD3, cholecalciferol) (Holick et al. 1977).
R-HSA-209760 (Reactome) The internalized CUBN:GC:25(OH)D complex enters the lysosome where it can be acted upon the protease legumain (Halfon et al. 1998, Chen et al. 2000).
R-HSA-209765 (Reactome) 1-alpha, 25-dihydroxyvitamin D (1,25(OH)2D) is biologically inactivated through a series of reactions beginning with 24-hydroxylation and is most likely a mechanism of elimination. 24-Hydroxylation of vitamin D metabolites is largely regulated inversely to 1-hydroxylation, the initial step towards activation (Chen et al. 1993).
R-HSA-209766 (Reactome) Once out of the lysosome, 25-hydroxyvitamin D (calcidiol, 25(OH)D) translocates to the mitochondion where it is made available to the mitochondrial membrane-resident protein CYP27B1 for further hydroxylation. The mechanism of mitochondrial targeting is unknown but may involve some kind of intracellular vitamin D binding protein (IDBP). IDBPs are related to the hsc-70 family of heat shock proteins and may function to localise vitamin D metabolites to specific areas. No human IDBP has yet been characterised (Radons 2016).
R-HSA-209845 (Reactome) To be functionally active, vitamin D3 (VD3) needs to be dihydroxylated. The first hydroxylation at position 25 is carried out by ER membrane-located vitamin D 25-hydroxylase (CYP2R1) in the liver, forming 25-hydroxyvitamin D (calcidiol, 25(OH)D) (Shinkyo et al. 2004, Cheng et al. 2003).
R-HSA-209868 (Reactome) The second step in vitamin D activation requires hydroxylation of 25-hydroxyvitamin D (calcidiol, 25(OH)D) to 1-alpha, 25-dihydroxyvitamin D (1,25(OH)2D). This conversion is mediated by 25-hydroxyvitamin D-1-alpha hydroxylase (CYP27B1), an outer mitochondrial membrane-resident protein (Zehnder et al. 2002, Fritsche et al. 2003, Sawada et al. 1999).
R-HSA-209944 (Reactome) Vitamin D binding protein (GC aka DBP), a plasma protein, carries vitamin D metabolites in the circulation. 25-hydroxyvitamin D (25(OH)D) translocates to the extracellular region where it binds with GC and is transported to the kidney (Verboven et al. 2002).
R-HSA-350147 (Reactome) Once vitamin D3 (VD3) is released from vitamin D binding protein (GC, DBP), it translocates from the extracellular region to the ER membrane, becoming available for hydroxylation by the microsomal enzyme CYP2R1 (Shinkyo et al. 2004).
R-HSA-350158 (Reactome) Mammalian legumain (LGMN, asparagine-specific endoprotease) is a subfamily of cysteine proteases with no homology to other known proteases and is found in a wide range of organisms from parasites to plants and animals. LGMN requires acidic conditions for its degradative activity. Cubilin (CUBN), once released from the complex, cycles back to the cell surface. Free 25-hydroxyvitamin D (calcidiol, 25(OH)D) becomes available for further processing (Nykjaer et al. 1999).
R-HSA-350168 (Reactome) Megalin (LRP2, glycoprotein 330) is a member of the low density lipoprotein receptor family and is abundant in kidney proximal tubules (Kounnas et al. 1995, Hjalm et al. 1996). LRP2 mediates the endocytic uptake of GC:25(OH)D complexes, thereby preventing the loss of 25-hydroxyvitamin D (calcidiol, 25(OH)D) in urine (Nykjaer et al. 1999, Kaseda et al. 2011).
R-HSA-350186 (Reactome) Cubilin (CUBN) is a membrane-associated protein colocalising with megalin (LRP2). Its function is to sequester steroid carrier complexes such as vitamin D binding protein:25-hydroxyvitamin D (GC:25(OH)D) on the cell surface before LRP2 mediates their internalisation (Nykjaer et al. 2001).
R-HSA-4546387 (Reactome) E3 SUMO-protein ligase (PIAS4) SUMOylates Vitamin D3 receptor (VDR) with SUMO2 (Jena et al. 2012). SUMOylation inhibits transcriptional activation by VDR in response to vitamin D.
R-HSA-6807242 (Reactome) 25-hydroxyvitamin D (calcidiol, 25(OH)D) translocates to the extracellular region (Verboven et al. 2002).
R-HSA-8963851 (Reactome) Vitamin D3 (VD3) is transported to the liver bound to a plasma protein called vitamin D binding protein (GC aka DBP) (Verboven et al. 2002). Before uptake by the liver, VD3 must dissociate from GC.
R-HSA-8963864 (Reactome) Cubilin (CUBN), once released from the complex, cycles back to the cell surface. Free 25-hydroxyvitamin D (calcidiol, 25(OH)D) becomes available for further processing (Nykjaer et al. 1999).
R-HSA-8963872 (Reactome) Vitamin D metabolites such as VD3 are lipophilic and must be transported in the circulation bound to plasma proteins. VD3 translocates to the extracellular region where it binds GC, a vitamin D binding protein (Verboven et al. 2002).
R-HSA-8963913 (Reactome) The biologically active form of vitamin D, 1-alpha, 25-dihydroxyvitamin D (1,25(OH)2D), can be transported to any target tissue where it enters the nucleoplasm to interact with vitamin D receptor (VDR) to exert its effects. The mechanism of translocation from cytosol to nucleoplasm is unknown (see review for general description - Christakos et al. 2016).
R-HSA-8963915 (Reactome) The biologically active form of vitamin D, 1-alpha, 25-dihydroxyvitamin D (1,25(OH)2D), interacts with the nuclear hormone receptor vitamin D receptor (VDR) in the nucleoplasm of any target tissue (Neme et al. 2017). VDR regulates the actions of 1,25(OH)2D and their binding recruits coactivators (Eelen et al. 2005, Kim et al. 2005, Du et al. 2017) to initiate a signaling response that regulates an estimated upwards of 2000 genes involved in calcium homeostasis, immune responses, cellular growth, differentiation and apoptosis (Hossein-nezhad et al. 2013, Hossein-nezhad & Holick 2013, Wolden-Kirk et al. 2012, Prietl et al. 2013, Hewison 2012, Christakos et al. 2016, Bandera Merchan et al. 2017).
SUMO2-VDRArrowR-HSA-4546387 (Reactome)
SUMO2:UBE2IR-HSA-4546387 (Reactome)
UBE2IArrowR-HSA-4546387 (Reactome)
VD3ArrowR-HSA-209754 (Reactome)
VD3ArrowR-HSA-350147 (Reactome)
VD3ArrowR-HSA-8963851 (Reactome)
VD3ArrowR-HSA-8963872 (Reactome)
VD3R-HSA-209738 (Reactome)
VD3R-HSA-209845 (Reactome)
VD3R-HSA-350147 (Reactome)
VD3R-HSA-8963872 (Reactome)
VDRR-HSA-4546387 (Reactome)
VDRR-HSA-8963915 (Reactome)
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