CPVDH_PSEAH
ID CPVDH_PSEAH Reviewed; 403 AA.
AC C4B644;
DT 22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 1.
DT 03-AUG-2022, entry version 51.
DE RecName: Full=Vitamin D(3) 25-hydroxylase {ECO:0000303|PubMed:19450562, ECO:0000312|EMBL:BAH58688.1};
DE EC=1.14.15.15 {ECO:0000269|PubMed:19450562};
DE AltName: Full=Cytochrome P450 {ECO:0000250|UniProtKB:P0A512};
GN Name=vdh {ECO:0000312|EMBL:BAH58688.1};
OS Pseudonocardia autotrophica (Amycolata autotrophica) (Nocardia
OS autotrophica).
OC Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
OC Pseudonocardia.
OX NCBI_TaxID=2074;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-28 AND 187-198,
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND MUTAGENESIS OF THR-70; VAL-156; GLU-216 AND GLU-384.
RC STRAIN=ATCC 19727 / DSM 535 / CBS 466.68 / JCM 4348 / NBRC 12743 / NCIMB
RC 9810 / NRRL B-11275 / ISP 5011;
RX PubMed=19450562; DOI=10.1016/j.bbrc.2009.05.033;
RA Fujii Y., Kabumoto H., Nishimura K., Fujii T., Yanai S., Takeda K.,
RA Tamura N., Arisawa A., Tamura T.;
RT "Purification, characterization, and directed evolution study of a vitamin
RT D3 hydroxylase from Pseudonocardia autotrophica.";
RL Biochem. Biophys. Res. Commun. 385:170-175(2009).
CC -!- FUNCTION: Hydroxylates vitamin D(3) into 25-hydroxyvitamin D(3) and 1-
CC alpha,25-dihydroxyvitamin D(3), its physiologically active forms. It
CC first hydroxylates the C-25 position of vitamin D(3) to form 25-
CC hydroxyvitamin D(3), then subsequently hydroxylates the C-1-alpha
CC position to form 1-alpha,25-dihydroxyvitamin D(3). Also displays 25-
CC hydroxylase activity on vitamin D(2) and 7-dehydrocholesterol. May play
CC a role in the biosynthesis of steroid metabolic intermediates.
CC {ECO:0000269|PubMed:19450562}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5beta-cholestane-3alpha,7alpha,12alpha-triol + 5 H(+) + 3 O2 +
CC 6 reduced [adrenodoxin] = (25R)-3alpha,7alpha,12alpha-trihydroxy-
CC 5beta-cholestan-26-oate + 4 H2O + 6 oxidized [adrenodoxin];
CC Xref=Rhea:RHEA:34631, Rhea:RHEA-COMP:9998, Rhea:RHEA-COMP:9999,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16496, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:58734; EC=1.14.15.15;
CC Evidence={ECO:0000269|PubMed:19450562};
CC -!- COFACTOR:
CC Name=heme; Xref=ChEBI:CHEBI:30413;
CC Evidence={ECO:0000250|UniProtKB:P0A512};
CC -!- ACTIVITY REGULATION: Activated by partially methylated beta-
CC cyclodextrin. {ECO:0000269|PubMed:19450562}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=13.5 uM for vitamin D(3) {ECO:0000269|PubMed:19450562};
CC KM=7.1 uM for 25-hydroxyvitamin D(3) {ECO:0000269|PubMed:19450562};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P0A512}.
CC -!- SIMILARITY: Belongs to the cytochrome P450 family. {ECO:0000255}.
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DR EMBL; AB456955; BAH58688.1; -; Genomic_DNA.
DR PDB; 3A4G; X-ray; 1.75 A; A=1-403.
DR PDB; 3A4H; X-ray; 3.06 A; A=1-403.
DR PDB; 3A4Z; X-ray; 2.20 A; A/B/C/D/E=1-403.
DR PDB; 3A50; X-ray; 2.05 A; A/B/C/D/E=1-403.
DR PDB; 3A51; X-ray; 2.00 A; A/B/C/D/E=1-403.
DR PDB; 3VRM; X-ray; 2.57 A; A=1-403.
DR PDB; 5GNL; X-ray; 1.95 A; A=1-403.
DR PDB; 5GNM; X-ray; 2.70 A; A/B/C/D=1-403.
DR PDBsum; 3A4G; -.
DR PDBsum; 3A4H; -.
DR PDBsum; 3A4Z; -.
DR PDBsum; 3A50; -.
DR PDBsum; 3A51; -.
DR PDBsum; 3VRM; -.
DR PDBsum; 5GNL; -.
DR PDBsum; 5GNM; -.
DR AlphaFoldDB; C4B644; -.
DR SMR; C4B644; -.
DR BRENDA; 1.14.14.24; 309.
DR SABIO-RK; C4B644; -.
DR EvolutionaryTrace; C4B644; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0047103; F:3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity; IEA:UniProtKB-EC.
DR GO; GO:0047748; F:cholestanetetraol 26-dehydrogenase activity; IEA:RHEA.
DR GO; GO:0047749; F:cholestanetriol 26-monooxygenase activity; IEA:UniProtKB-EC.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR Gene3D; 1.10.630.10; -; 1.
DR InterPro; IPR001128; Cyt_P450.
DR InterPro; IPR002397; Cyt_P450_B.
DR InterPro; IPR017972; Cyt_P450_CS.
DR InterPro; IPR036396; Cyt_P450_sf.
DR Pfam; PF00067; p450; 1.
DR PRINTS; PR00359; BP450.
DR SUPFAM; SSF48264; SSF48264; 1.
DR PROSITE; PS00086; CYTOCHROME_P450; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Heme; Iron;
KW Metal-binding; Monooxygenase; Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:19450562"
FT CHAIN 2..403
FT /note="Vitamin D(3) 25-hydroxylase"
FT /evidence="ECO:0000269|PubMed:19450562"
FT /id="PRO_0000383672"
FT BINDING 347
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250|UniProtKB:P0A512"
FT MUTAGEN 70
FT /note="T->R: Increases 25-hydroxylase activity 2.0-fold.
FT Increases 25-hydroxylase activity 21.6-fold; when
FT associated with V156L, E216M and E348R."
FT /evidence="ECO:0000269|PubMed:19450562"
FT MUTAGEN 156
FT /note="V->L: Increases 25-hydroxylase activity 21.6-fold;
FT when associated with T70R; E216M and E348R."
FT /evidence="ECO:0000269|PubMed:19450562"
FT MUTAGEN 156
FT /note="V->S: Increases 25-hydroxylase activity 2.5-fold."
FT /evidence="ECO:0000269|PubMed:19450562"
FT MUTAGEN 216
FT /note="E->A: Increases 25-hydroxylase activity 1.9-fold."
FT /evidence="ECO:0000269|PubMed:19450562"
FT MUTAGEN 216
FT /note="E->M: Increases 25-hydroxylase activity 21.6-fold;
FT when associated with T70R; V156L and E348R."
FT /evidence="ECO:0000269|PubMed:19450562"
FT MUTAGEN 384
FT /note="E->R: Increases 25-hydroxylase activity 2.8-fold.
FT Increases 25-hydroxylase activity 21.6-fold; when
FT associated with T70R; V156L and E216M."
FT /evidence="ECO:0000269|PubMed:19450562"
FT CONFLICT 4..6
FT /note="Missing (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 17
FT /note="T -> F (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 23..25
FT /note="HPA -> QPP (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:5GNM"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 23..32
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 51..58
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:3A4G"
FT TURN 76..78
FT /evidence="ECO:0007829|PDB:3A51"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 94..103
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:3VRM"
FT HELIX 108..128
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 137..140
FT /evidence="ECO:0007829|PDB:3A4G"
FT TURN 141..144
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 145..154
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 161..171
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:5GNL"
FT TURN 177..179
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 180..200
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 206..212
FT /evidence="ECO:0007829|PDB:3A4G"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:3A51"
FT HELIX 223..237
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 239..253
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 256..264
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 266..268
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 269..279
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 282..285
FT /evidence="ECO:0007829|PDB:5GNM"
FT STRAND 289..293
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 300..302
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 307..311
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 312..315
FT /evidence="ECO:0007829|PDB:3A4G"
FT TURN 319..321
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 338..340
FT /evidence="ECO:0007829|PDB:5GNM"
FT HELIX 343..345
FT /evidence="ECO:0007829|PDB:3A51"
FT HELIX 350..367
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 372..375
FT /evidence="ECO:0007829|PDB:3A4G"
FT HELIX 377..379
FT /evidence="ECO:0007829|PDB:3A4G"
FT STRAND 386..388
FT /evidence="ECO:0007829|PDB:3A51"
FT STRAND 395..397
FT /evidence="ECO:0007829|PDB:3A4G"
SQ SEQUENCE 403 AA; 44369 MW; 5984C6AE5AA1C756 CRC64;
MALTTTGTEQ HDLFSGTFWQ NPHPAYAALR AEDPVRKLAL PDGPVWLLTR YADVREAFVD
PRLSKDWRHT LPEDQRADMP ATPTPMMILM DPPDHTRLRK LVGRSFTVRR MNELEPRITE
IADGLLAGLP TDGPVDLMRE YAFQIPVQVI CELLGVPAED RDDFSAWSSV LVDDSPADDK
NAAMGKLHGY LSDLLERKRT EPDDALLSSL LAVSDEDGDR LSQEELVAMA MLLLIAGHET
TVNLIGNGVL ALLTHPDQRK LLAEDPSLIS SAVEEFLRFD SPVSQAPIRF TAEDVTYSGV
TIPAGEMVML GLAAANRDAD WMPEPDRLDI TRDASGGVFF GHGIHFCLGA QLARLEGRVA
IGRLFADRPE LALAVGLDEL VYRESTLVRG LSRMPVTMGP RSA
