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Vitamin D3 dihydroxylase (EC 1.14.15.22) (CYP105A1) (Cytochrome P450-CVA1) (Cytochrome P450-SU1) (Vitamin D3 hydroxylase) (VD3 hydroxylase)

 CPXE_STRGO              Reviewed;         406 AA.
P18326;
01-NOV-1990, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
25-OCT-2017, entry version 95.
RecName: Full=Vitamin D3 dihydroxylase {ECO:0000305};
EC=1.14.15.22 {ECO:0000269|PubMed:15207715, ECO:0000269|PubMed:18314962, ECO:0000269|PubMed:18937506};
AltName: Full=CYP105A1 {ECO:0000303|PubMed:2345149};
AltName: Full=Cytochrome P450-CVA1 {ECO:0000303|PubMed:2345149};
AltName: Full=Cytochrome P450-SU1 {ECO:0000303|PubMed:2345149};
AltName: Full=Vitamin D3 hydroxylase {ECO:0000303|PubMed:18937506};
Short=VD3 hydroxylase {ECO:0000303|PubMed:18937506};
Name=cyp105A1 {ECO:0000303|PubMed:2345149};
Synonyms=suaC {ECO:0000303|PubMed:2345149};
Streptomyces griseolus.
Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
Streptomyces.
NCBI_TaxID=1909;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-32, AND
INDUCTION.
STRAIN=ATCC 11796 / DSM 40854;
PubMed=2345149; DOI=10.1128/jb.172.6.3335-3345.1990;
Omer C.A., Lenstra R., Litle P.J., Dean C., Tepperman J.M., Leto K.J.,
Romesser J.A., O'Keefe D.P.;
"Genes for two herbicide-inducible cytochromes P-450 from Streptomyces
griseolus.";
J. Bacteriol. 172:3335-3345(1990).
[2]
PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, COFACTOR, AND
SUBSTRATE SPECIFICITY.
PubMed=15207715; DOI=10.1016/j.bbrc.2004.05.140;
Sawada N., Sakaki T., Yoneda S., Kusudo T., Shinkyo R., Ohta M.,
Inouye K.;
"Conversion of vitamin D3 to 1alpha,25-dihydroxyvitamin D3 by
Streptomyces griseolus cytochrome P450SU-1.";
Biochem. Biophys. Res. Commun. 320:156-164(2004).
[3]
X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-84
IN COMPLEX WITH HEME AND CALCITRIOL, FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ARG-73; ARG-84; VAL-88;
LEU-180; VAL-181; ARG-193 AND ILE-293, AND COFACTOR.
PubMed=18314962; DOI=10.1021/bi7023767;
Sugimoto H., Shinkyo R., Hayashi K., Yoneda S., Yamada M.,
Kamakura M., Ikushiro S., Shiro Y., Sakaki T.;
"Crystal structure of CYP105A1 (P450SU-1) in complex with 1alpha,25-
dihydroxyvitamin D3.";
Biochemistry 47:4017-4027(2008).
[4]
X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF MUTANT PHE-84 AND DOUBLE
MUTANT ALA-73/ALA-84 IN COMPLEX WITH HEME AND CALCITRIOL, FUNCTION,
CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF
ARG-73 AND ARG-84, AND COFACTOR.
PubMed=18937506; DOI=10.1021/bi801222d;
Hayashi K., Sugimoto H., Shinkyo R., Yamada M., Ikeda S., Ikushiro S.,
Kamakura M., Shiro Y., Sakaki T.;
"Structure-based design of a highly active vitamin D hydroxylase from
Streptomyces griseolus CYP105A1.";
Biochemistry 47:11964-11972(2008).
-!- FUNCTION: Involved in the metabolism of vitamin D3 (calciol) and
of a number of sulfonylurea herbicides. Catalyzes the two-step
hydroxylation (25- and 1-alpha-hydroxylation) of vitamin D3 (VD3)
to yield its active form 1-alpha,25-dihydroxyvitamin D3
(calcitriol). The first step is the hydroxylation of the C-25
position of VD3 to produce 25-hydroxyvitamin D3 (calcidiol). The
second reaction is the hydroxylation of the C1-alpha-position of
calcidiol to produce calcitriol. It can also hydroxylate vitamin
D2. {ECO:0000269|PubMed:15207715, ECO:0000269|PubMed:18314962,
ECO:0000269|PubMed:18937506}.
-!- CATALYTIC ACTIVITY: Calciol + O(2) + 2 reduced ferredoxin [iron-
sulfur] cluster + 2 H(+) = calcidiol + 2 oxidized ferredoxin
[iron-sulfur] cluster + H(2)O. {ECO:0000269|PubMed:15207715,
ECO:0000269|PubMed:18314962, ECO:0000269|PubMed:18937506}.
-!- CATALYTIC ACTIVITY: Calcidiol + 2 reduced ferredoxin [iron-sulfur]
cluster + 2 H(+) + O(2) = calcitriol + 2 oxidized ferredoxin
[iron-sulfur] cluster + H(2)O. {ECO:0000269|PubMed:15207715,
ECO:0000269|PubMed:18314962, ECO:0000269|PubMed:18937506}.
-!- COFACTOR:
Name=heme; Xref=ChEBI:CHEBI:30413;
Evidence={ECO:0000269|PubMed:15207715,
ECO:0000269|PubMed:18314962, ECO:0000269|PubMed:18937506};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.54 uM for vitamin D3 (at pH 7.4 and 30 degrees Celsius)
{ECO:0000269|PubMed:15207715};
KM=0.59 uM for vitamin D2 (at pH 7.4 and 30 degrees Celsius)
{ECO:0000269|PubMed:15207715};
KM=0.91 uM for 25-hydroxyvitamin D3 (1-alpha-hydroxylation)(at
pH 7.4 and 30 degrees Celsius) {ECO:0000269|PubMed:15207715};
KM=4.4 uM for 25-hydroxyvitamin D3 (1-alpha-hydroxylation)
{ECO:0000269|PubMed:18937506};
KM=5 uM for 25-hydroxyvitamin D3 (1-alpha-hydroxylation)
{ECO:0000269|PubMed:18314962};
KM=9.4 uM for 1-alpha-hydroxyvitamin D3 (25-alpha-hydroxylation)
{ECO:0000269|PubMed:18314962};
KM=10.1 uM for 1-alpha-hydroxyvitamin D3 (25-alpha-
hydroxylation) {ECO:0000269|PubMed:18937506};
Vmax=8.4 umol/min/mg enzyme with 25-hydroxyvitamin D3 as
substrate (1-alpha-hydroxylation) {ECO:0000269|PubMed:18314962};
Vmax=3.8 umol/min/mg enzyme with as 1-alpha-hydroxyvitamin D3
substrate (25-alpha-hydroxylation)
{ECO:0000269|PubMed:18314962};
Vmax=3.6 mmol/min/mg enzyme with 25-hydroxyvitamin D3 as
substrate (1-alpha-hydroxylation)(at pH 7.4 and 30 degrees
Celsius) {ECO:0000269|PubMed:15207715};
Vmax=16 mmol/min/mg enzyme with vitamin D3 as substrate (at pH
7.4 and 30 degrees Celsius) {ECO:0000269|PubMed:15207715};
Vmax=84 mmol/min/mg enzyme with vitamin D2 as substrate (at pH
7.4 and 30 degrees Celsius) {ECO:0000269|PubMed:15207715};
Note=Kcat is 0.0076 min(-1) for hydroxylase activity with 1-
alpha-hydroxyvitamin D3 as substrate. Kcat is 0.0026 min(-1) for
hydroxylase activity with 25-hydroxyvitamin D3 as substrate.
{ECO:0000269|PubMed:18937506};
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:15207715}.
-!- INDUCTION: By herbicides. {ECO:0000269|PubMed:2345149}.
-!- MISCELLANEOUS: Two metabolic pathways exist. One is a conversion
of VD3 to 25-hydroxyvitamin D3 and then to 1-alpha,25-
dihydroxyvitamin D3 (25-pathway), while the other one is a pathway
via 1-alpha-hydroxyvitamin D3 as an intermediate (1-alpha-
pathway). Analysis show that the amount of 25-hydroxyvitamin D3 is
predominant as the product of this reaction, while very small
amounts of 1-alpha-hydroxyvitamin D3 and 1-alpha,25-
dihydroxyvitamin D3 are obtained, suggesting that the major
pathway is the 25-pathway. {ECO:0000269|PubMed:18937506}.
-!- MISCELLANEOUS: The hydrophobicity and the volume of the side chain
at position 84 are critical for the activity.
{ECO:0000269|PubMed:18937506}.
-!- SIMILARITY: Belongs to the cytochrome P450 family. {ECO:0000305}.
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EMBL; M32238; AAA26823.1; -; Genomic_DNA.
PIR; A35401; A35401.
PDB; 2ZBX; X-ray; 1.50 A; A=1-406.
PDB; 2ZBY; X-ray; 1.60 A; A=1-406.
PDB; 2ZBZ; X-ray; 1.90 A; A=1-406.
PDB; 3CV8; X-ray; 2.00 A; A=1-406.
PDB; 3CV9; X-ray; 1.70 A; A=1-406.
PDB; 5X7E; X-ray; 1.90 A; A=1-406.
PDBsum; 2ZBX; -.
PDBsum; 2ZBY; -.
PDBsum; 2ZBZ; -.
PDBsum; 3CV8; -.
PDBsum; 3CV9; -.
PDBsum; 5X7E; -.
ProteinModelPortal; P18326; -.
SMR; P18326; -.
KEGG; ag:AAA26823; -.
KO; K21146; -.
EvolutionaryTrace; P18326; -.
GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
GO; GO:0020037; F:heme binding; IDA:UniProtKB.
GO; GO:0005506; F:iron ion binding; IEA:InterPro.
GO; GO:0016709; F:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen; IDA:UniProtKB.
GO; GO:0070640; P:vitamin D3 metabolic process; IDA:UniProtKB.
Gene3D; 1.10.630.10; -; 1.
InterPro; IPR001128; Cyt_P450.
InterPro; IPR002397; Cyt_P450_B.
InterPro; IPR017972; Cyt_P450_CS.
InterPro; IPR036396; Cyt_P450_sf.
Pfam; PF00067; p450; 1.
PRINTS; PR00359; BP450.
PRINTS; PR00385; P450.
SUPFAM; SSF48264; SSF48264; 1.
PROSITE; PS00086; CYTOCHROME_P450; 1.
1: Evidence at protein level;
3D-structure; Cytoplasm; Direct protein sequencing; Heme; Iron;
Metal-binding; Monooxygenase; NADP; Oxidoreductase.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:15207715,
ECO:0000269|PubMed:2345149}.
CHAIN 2 406 Vitamin D3 dihydroxylase.
/FTId=PRO_0000052213.
METAL 355 355 Iron (heme axial ligand).
{ECO:0000269|PubMed:18314962}.
BINDING 81 81 Vitamin D3.
{ECO:0000269|PubMed:18937506}.
BINDING 103 103 Heme. {ECO:0000269|PubMed:18314962}.
BINDING 107 107 Heme. {ECO:0000269|PubMed:18314962}.
BINDING 193 193 Vitamin D3. {ECO:0000269|PubMed:18314962,
ECO:0000269|PubMed:18937506}.
BINDING 236 236 Vitamin D3.
{ECO:0000269|PubMed:18314962}.
BINDING 293 293 Vitamin D3; via carbonyl oxygen.
{ECO:0000269|PubMed:18314962,
ECO:0000269|PubMed:18937506}.
BINDING 297 297 Heme. {ECO:0000269|PubMed:18314962}.
BINDING 353 353 Heme. {ECO:0000269|PubMed:18314962}.
MUTAGEN 73 73 R->A,F,L,V: Increase of the hydroxylase
activity and decrease of affinity for
both 25-hydroxyvitamin D3 and 1-alpha-
hydroxyvitamin D3. Increase of the
hydroxylase activity; when associated
with A-84 and F-84.
{ECO:0000269|PubMed:18314962,
ECO:0000269|PubMed:18937506}.
MUTAGEN 84 84 R->A,Q,L,F: Increase of the hydroxylase
activity and decrease of affinity for
both 25-hydroxyvitamin D3 and 1-alpha-
hydroxyvitamin D3. Increase of the
hydroxylase activity; when associated
with A-73 and V-73.
{ECO:0000269|PubMed:18314962}.
MUTAGEN 84 84 R->F: Alters the substrate specificity
that gives preference to the 1-alpha-
hydroxylation of 25-hydroxyvitamin D3
over the 25-hydroxylation of 1-alpha-
hydroxyvitamin D3. Increase of the
hydroxylase activity and decrease of
affinity for both 25-hydroxyvitamin D3
and 1-alpha-hydroxyvitamin D3.
{ECO:0000269|PubMed:18937506}.
MUTAGEN 88 88 V->A: Decrease of the hydroxylase
activity for both 25-hydroxyivitamin D3
and 1-alpha-hydroxyvitamin D3.
{ECO:0000269|PubMed:18314962}.
MUTAGEN 180 180 L->A: Decrease of the hydroxylase
activity for both 25-hydroxyvitamin D3
and 1-alpha-hydroxyvitamin D3.
{ECO:0000269|PubMed:18314962}.
MUTAGEN 181 181 V->A: Decrease of the hydroxylase
activity for both 25-hydroxyvitamin D3
and 1-alpha-hydroxyvitamin D3.
{ECO:0000269|PubMed:18314962}.
MUTAGEN 193 193 R->A,Q,K: Decrease of the hydroxylase
activity. {ECO:0000269|PubMed:18314962}.
MUTAGEN 293 293 I->A: Slight increase of the hydroxylase
activity. {ECO:0000269|PubMed:18314962}.
STRAND 15 17 {ECO:0000244|PDB:2ZBX}.
HELIX 28 35 {ECO:0000244|PDB:2ZBX}.
STRAND 36 44 {ECO:0000244|PDB:2ZBX}.
STRAND 50 54 {ECO:0000244|PDB:2ZBX}.
HELIX 57 64 {ECO:0000244|PDB:2ZBX}.
HELIX 83 85 {ECO:0000244|PDB:2ZBX}.
TURN 88 90 {ECO:0000244|PDB:2ZBY}.
HELIX 95 97 {ECO:0000244|PDB:2ZBX}.
HELIX 102 107 {ECO:0000244|PDB:2ZBX}.
TURN 108 110 {ECO:0000244|PDB:2ZBX}.
HELIX 111 114 {ECO:0000244|PDB:2ZBX}.
HELIX 116 140 {ECO:0000244|PDB:2ZBX}.
STRAND 142 145 {ECO:0000244|PDB:2ZBY}.
HELIX 146 149 {ECO:0000244|PDB:2ZBX}.
TURN 150 152 {ECO:0000244|PDB:2ZBX}.
HELIX 153 163 {ECO:0000244|PDB:2ZBX}.
HELIX 167 169 {ECO:0000244|PDB:2ZBX}.
HELIX 170 182 {ECO:0000244|PDB:2ZBX}.
HELIX 186 209 {ECO:0000244|PDB:2ZBX}.
HELIX 215 221 {ECO:0000244|PDB:2ZBX}.
TURN 222 227 {ECO:0000244|PDB:2ZBX}.
HELIX 231 261 {ECO:0000244|PDB:2ZBX}.
HELIX 264 272 {ECO:0000244|PDB:2ZBX}.
HELIX 274 276 {ECO:0000244|PDB:2ZBX}.
HELIX 277 288 {ECO:0000244|PDB:2ZBX}.
HELIX 292 294 {ECO:0000244|PDB:2ZBX}.
STRAND 296 301 {ECO:0000244|PDB:2ZBX}.
STRAND 303 305 {ECO:0000244|PDB:2ZBX}.
STRAND 308 310 {ECO:0000244|PDB:2ZBX}.
STRAND 315 318 {ECO:0000244|PDB:2ZBX}.
HELIX 320 323 {ECO:0000244|PDB:2ZBX}.
TURN 327 329 {ECO:0000244|PDB:2ZBX}.
STRAND 330 332 {ECO:0000244|PDB:2ZBX}.
HELIX 358 375 {ECO:0000244|PDB:2ZBX}.
STRAND 380 383 {ECO:0000244|PDB:2ZBX}.
HELIX 385 387 {ECO:0000244|PDB:2ZBX}.
STRAND 398 400 {ECO:0000244|PDB:3CV9}.
STRAND 403 405 {ECO:0000244|PDB:2ZBX}.
SEQUENCE 406 AA; 44212 MW; B41CDD7B9BC56191 CRC64;
MTDTATTPQT TDAPAFPSNR SCPYQLPDGY AQLRDTPGPL HRVTLYDGRQ AWVVTKHEAA
RKLLGDPRLS SNRTDDNFPA TSPRFEAVRE SPQAFIGLDP PEHGTRRRMT ISEFTVKRIK
GMRPEVEEVV HGFLDEMLAA GPTADLVSQF ALPVPSMVIC RLLGVPYADH EFFQDASKRL
VQSTDAQSAL TARNDLAGYL DGLITQFQTE PGAGLVGALV ADQLANGEID REELISTAML
LLIAGHETTA SMTSLSVITL LDHPEQYAAL RADRSLVPGA VEELLRYLAI ADIAGGRVAT
ADIEVEGHLI RAGEGVIVVN SIANRDGTVY EDPDALDIHR SARHHLAFGF GVHQCLGQNL
ARLELEVILN ALMDRVPTLR LAVPVEQLVL RPGTTIQGVN ELPVTW


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