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Vitamin D 25-hydroxylase (EC 1.14.14.24) (Cytochrome P450 2R1)

 CP2R1_HUMAN             Reviewed;         501 AA.
Q6VVX0; Q2M3H3; Q5RT65;
29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
05-JUL-2004, sequence version 1.
28-MAR-2018, entry version 136.
RecName: Full=Vitamin D 25-hydroxylase;
EC=1.14.14.24 {ECO:0000269|PubMed:12867411, ECO:0000269|PubMed:15465040, ECO:0000269|PubMed:18511070};
AltName: Full=Cytochrome P450 2R1;
Name=CYP2R1;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=12867411; DOI=10.1074/jbc.M307028200;
Cheng J.B., Motola D.L., Mangelsdorf D.J., Russell D.W.;
"De-orphanization of cytochrome P450 2R1: a microsomal vitamin D 25-
hydroxylase.";
J. Biol. Chem. 278:38084-38093(2003).
[2]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, AND
BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=15465040; DOI=10.1016/j.bbrc.2004.09.073;
Shinkyo R., Sakaki T., Kamakura M., Ohta M., Inouye K.;
"Metabolism of vitamin D by human microsomal CYP2R1.";
Biochem. Biophys. Res. Commun. 324:451-457(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Liver;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-8.
Tsuruga E., Bell N.H., Reddy S.V.;
"Human CYP2R1 gene 5'-flanking region.";
Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
[5]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 32-501 IN COMPLEX WITH
VITAMIN D3 AND HEME, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
PROPERTIES, AND SUBUNIT.
PubMed=18511070; DOI=10.1016/j.jmb.2008.03.065;
Strushkevich N., Usanov S.A., Plotnikov A.N., Jones G., Park H.-W.;
"Structural analysis of CYP2R1 in complex with vitamin D3.";
J. Mol. Biol. 380:95-106(2008).
[6]
X-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS) OF 32-501 IN COMPLEXES WITH
HEME; VITAMIN D2 AND 1-ALPHA-HYDROXY-VITAMIN D2.
Structural genomics consortium (SGC);
"Crystal structure of CYP2R1 in complexes with 1-alpha-hydroxy-vitamin
D2 and with vitamin D2.";
Submitted (FEB-2009) to the PDB data bank.
[7]
VARIANT VDDR1B PRO-99.
PubMed=15128933; DOI=10.1073/pnas.0402490101;
Cheng J.B., Levine M.A., Bell N.H., Mangelsdorf D.J., Russell D.W.;
"Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-
hydroxylase.";
Proc. Natl. Acad. Sci. U.S.A. 101:7711-7715(2004).
[8]
VARIANT VDDR1B PRO-99, VARIANT ASN-242, CHARACTERIZATION OF VARIANT
VDDR1B PRO-99, AND CHARACTERIZATION OF VARIANT ASN-242.
PubMed=25942481; DOI=10.1210/jc.2015-1746;
Thacher T.D., Fischer P.R., Singh R.J., Roizen J., Levine M.A.;
"CYP2R1 mutations impair generation of 25-hydroxyvitamin D and cause
an atypical form of vitamin D deficiency.";
J. Clin. Endocrinol. Metab. 100:E1005-1013(2015).
-!- FUNCTION: Has a D-25-hydroxylase activity on both forms of vitamin
D, vitamin D(2) and D(3). {ECO:0000269|PubMed:12867411,
ECO:0000269|PubMed:15465040, ECO:0000269|PubMed:18511070}.
-!- CATALYTIC ACTIVITY: Calciol + O(2) + [reduced NADPH--hemoprotein
reductase] = calcidiol + [oxidized NADPH--hemoprotein reductase] +
H(2)O. {ECO:0000269|PubMed:12867411, ECO:0000269|PubMed:15465040,
ECO:0000269|PubMed:18511070}.
-!- COFACTOR:
Name=heme; Xref=ChEBI:CHEBI:30413; Evidence={ECO:0000250};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.67 uM for vitamin D(2) {ECO:0000269|PubMed:15465040,
ECO:0000269|PubMed:18511070};
KM=0.45 uM for vitamin D(3) {ECO:0000269|PubMed:15465040,
ECO:0000269|PubMed:18511070};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18511070}.
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Peripheral
membrane protein. Microsome membrane; Peripheral membrane protein.
-!- DISEASE: Rickets vitamin D-dependent 1B (VDDR1B) [MIM:600081]: An
autosomal recessive disorder caused by a selective deficiency of
the active form of vitamin D (1,25-dihydroxyvitamin D3) and
resulting in defective bone mineralization and clinical features
of rickets. The patients sera have low calcium concentrations, low
phosphate concentrations, elevated alkaline phosphatase activity
and low levels of 25-hydroxyvitamin D.
{ECO:0000269|PubMed:15128933, ECO:0000269|PubMed:25942481}.
Note=The disease is caused by mutations affecting the gene
represented in this entry.
-!- SIMILARITY: Belongs to the cytochrome P450 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AY323817; AAQ23114.1; -; mRNA.
EMBL; BC104907; AAI04908.1; -; mRNA.
EMBL; BC104909; AAI04910.1; -; mRNA.
EMBL; AY800276; AAV65814.1; -; Genomic_DNA.
CCDS; CCDS7818.1; -.
RefSeq; NP_078790.2; NM_024514.4.
UniGene; Hs.371427; -.
PDB; 3C6G; X-ray; 2.80 A; A/B=32-501.
PDB; 3CZH; X-ray; 2.30 A; A/B=32-501.
PDB; 3DL9; X-ray; 2.72 A; A/B=32-501.
PDBsum; 3C6G; -.
PDBsum; 3CZH; -.
PDBsum; 3DL9; -.
ProteinModelPortal; Q6VVX0; -.
SMR; Q6VVX0; -.
STRING; 9606.ENSP00000334592; -.
DrugBank; DB00169; Cholecalciferol.
DrugBank; DB00153; Ergocalciferol.
SwissLipids; SLP:000001264; -.
iPTMnet; Q6VVX0; -.
PhosphoSitePlus; Q6VVX0; -.
BioMuta; CYP2R1; -.
DMDM; 62286619; -.
PaxDb; Q6VVX0; -.
PeptideAtlas; Q6VVX0; -.
PRIDE; Q6VVX0; -.
Ensembl; ENST00000334636; ENSP00000334592; ENSG00000186104.
GeneID; 120227; -.
KEGG; hsa:120227; -.
UCSC; uc001mlr.4; human.
CTD; 120227; -.
DisGeNET; 120227; -.
EuPathDB; HostDB:ENSG00000186104.10; -.
GeneCards; CYP2R1; -.
HGNC; HGNC:20580; CYP2R1.
HPA; HPA042949; -.
MalaCards; CYP2R1; -.
MIM; 600081; phenotype.
MIM; 608713; gene.
neXtProt; NX_Q6VVX0; -.
OpenTargets; ENSG00000186104; -.
Orphanet; 289157; Hypocalcemic vitamin D-dependent rickets.
PharmGKB; PA134986407; -.
eggNOG; KOG0156; Eukaryota.
eggNOG; COG2124; LUCA.
GeneTree; ENSGT00900000140799; -.
HOGENOM; HOG000036991; -.
HOVERGEN; HBG015789; -.
InParanoid; Q6VVX0; -.
KO; K07419; -.
OMA; RFTYEDT; -.
OrthoDB; EOG091G0BT8; -.
PhylomeDB; Q6VVX0; -.
TreeFam; TF352043; -.
BioCyc; MetaCyc:HS17721-MONOMER; -.
BRENDA; 1.14.13.159; 2681.
Reactome; R-HSA-196791; Vitamin D (calciferol) metabolism.
Reactome; R-HSA-211916; Vitamins.
Reactome; R-HSA-5579027; Defective CYP2R1 causes Rickets vitamin D-dependent 1B (VDDR1B).
SABIO-RK; Q6VVX0; -.
EvolutionaryTrace; Q6VVX0; -.
GeneWiki; CYP2R1; -.
GenomeRNAi; 120227; -.
PRO; PR:Q6VVX0; -.
Proteomes; UP000005640; Chromosome 11.
Bgee; ENSG00000186104; -.
CleanEx; HS_CYP2R1; -.
ExpressionAtlas; Q6VVX0; baseline and differential.
Genevisible; Q6VVX0; HS.
GO; GO:0005789; C:endoplasmic reticulum membrane; TAS:Reactome.
GO; GO:0031090; C:organelle membrane; IEA:UniProtKB-SubCell.
GO; GO:0020037; F:heme binding; IEA:InterPro.
GO; GO:0005506; F:iron ion binding; IEA:InterPro.
GO; GO:0016705; F:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen; IEA:InterPro.
GO; GO:0008395; F:steroid hydroxylase activity; IBA:GO_Central.
GO; GO:0030343; F:vitamin D3 25-hydroxylase activity; TAS:Reactome.
GO; GO:0010164; P:response to cesium ion; IEA:Ensembl.
GO; GO:0010212; P:response to ionizing radiation; IEA:Ensembl.
GO; GO:0042359; P:vitamin D metabolic process; TAS:Reactome.
GO; GO:0006766; P:vitamin metabolic process; TAS:Reactome.
Gene3D; 1.10.630.10; -; 1.
InterPro; IPR001128; Cyt_P450.
InterPro; IPR017972; Cyt_P450_CS.
InterPro; IPR002401; Cyt_P450_E_grp-I.
InterPro; IPR036396; Cyt_P450_sf.
Pfam; PF00067; p450; 1.
PRINTS; PR00463; EP450I.
PRINTS; PR00385; P450.
SUPFAM; SSF48264; SSF48264; 1.
PROSITE; PS00086; CYTOCHROME_P450; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Disease mutation;
Endoplasmic reticulum; Heme; Iron; Membrane; Metal-binding; Microsome;
Monooxygenase; Oxidoreductase; Reference proteome.
CHAIN 1 501 Vitamin D 25-hydroxylase.
/FTId=PRO_0000051778.
METAL 448 448 Iron (heme axial ligand).
BINDING 250 250 Substrate; via carbonyl oxygen.
VARIANT 99 99 L -> P (in VDDR1B; complete loss of
activity; dbSNP:rs61495246).
{ECO:0000269|PubMed:15128933,
ECO:0000269|PubMed:25942481}.
/FTId=VAR_021534.
VARIANT 242 242 K -> N (reduces 25-hydroxylase activity).
{ECO:0000269|PubMed:25942481}.
/FTId=VAR_075532.
TURN 47 49 {ECO:0000244|PDB:3CZH}.
HELIX 52 57 {ECO:0000244|PDB:3CZH}.
HELIX 62 73 {ECO:0000244|PDB:3CZH}.
STRAND 75 81 {ECO:0000244|PDB:3CZH}.
STRAND 84 91 {ECO:0000244|PDB:3CZH}.
HELIX 92 99 {ECO:0000244|PDB:3CZH}.
TURN 100 106 {ECO:0000244|PDB:3CZH}.
HELIX 113 119 {ECO:0000244|PDB:3CZH}.
HELIX 131 146 {ECO:0000244|PDB:3CZH}.
TURN 147 150 {ECO:0000244|PDB:3CZH}.
HELIX 154 170 {ECO:0000244|PDB:3CZH}.
TURN 171 174 {ECO:0000244|PDB:3CZH}.
HELIX 180 196 {ECO:0000244|PDB:3CZH}.
HELIX 205 220 {ECO:0000244|PDB:3CZH}.
HELIX 224 231 {ECO:0000244|PDB:3CZH}.
HELIX 233 237 {ECO:0000244|PDB:3CZH}.
STRAND 239 241 {ECO:0000244|PDB:3CZH}.
HELIX 242 265 {ECO:0000244|PDB:3CZH}.
HELIX 276 286 {ECO:0000244|PDB:3CZH}.
TURN 287 289 {ECO:0000244|PDB:3CZH}.
HELIX 297 328 {ECO:0000244|PDB:3CZH}.
HELIX 330 343 {ECO:0000244|PDB:3CZH}.
STRAND 346 348 {ECO:0000244|PDB:3CZH}.
HELIX 352 357 {ECO:0000244|PDB:3CZH}.
HELIX 359 372 {ECO:0000244|PDB:3CZH}.
STRAND 387 389 {ECO:0000244|PDB:3CZH}.
STRAND 392 394 {ECO:0000244|PDB:3CZH}.
STRAND 399 403 {ECO:0000244|PDB:3CZH}.
HELIX 404 408 {ECO:0000244|PDB:3CZH}.
TURN 411 413 {ECO:0000244|PDB:3CZH}.
STRAND 414 416 {ECO:0000244|PDB:3C6G}.
HELIX 422 425 {ECO:0000244|PDB:3CZH}.
HELIX 451 468 {ECO:0000244|PDB:3CZH}.
STRAND 469 472 {ECO:0000244|PDB:3CZH}.
HELIX 474 476 {ECO:0000244|PDB:3CZH}.
STRAND 485 488 {ECO:0000244|PDB:3CZH}.
STRAND 496 500 {ECO:0000244|PDB:3CZH}.
SEQUENCE 501 AA; 57359 MW; F05E5245C580C29E CRC64;
MWKLWRAEEG AAALGGALFL LLFALGVRQL LKQRRPMGFP PGPPGLPFIG NIYSLAASSE
LPHVYMRKQS QVYGEIFSLD LGGISTVVLN GYDVVKECLV HQSEIFADRP CLPLFMKMTK
MGGLLNSRYG RGWVDHRRLA VNSFRYFGYG QKSFESKILE ETKFFNDAIE TYKGRPFDFK
QLITNAVSNI TNLIIFGERF TYEDTDFQHM IELFSENVEL AASASVFLYN AFPWIGILPF
GKHQQLFRNA AVVYDFLSRL IEKASVNRKP QLPQHFVDAY LDEMDQGKND PSSTFSKENL
IFSVGELIIA GTETTTNVLR WAILFMALYP NIQGQVQKEI DLIMGPNGKP SWDDKCKMPY
TEAVLHEVLR FCNIVPLGIF HATSEDAVVR GYSIPKGTTV ITNLYSVHFD EKYWRDPEVF
HPERFLDSSG YFAKKEALVP FSLGRRHCLG EHLARMEMFL FFTALLQRFH LHFPHELVPD
LKPRLGMTLQ PQPYLICAER R


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