Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Vitamin D(3) 25-hydroxylase

Gene

vdh

Organism
Pseudonocardia autotrophica (Amycolata autotrophica) (Nocardia autotrophica)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Hydroxylates vitamin D3 into 25-hydroxyvitamin D3 and 1-alpha,25-dihydroxyvitamin D3, its physiologically active forms. It first hydroxylates the C-25 position of vitamin D3 to form 25-hydroxyvitamin D3, then subsequently hydroxylates the C-1-alpha position to form 1-alpha,25-dihydroxyvitamin D3. Also displays 25-hydroxylase activity on vitamin D2 and 7-dehydrocholesterol. May play a role in the biosynthesis of steroid metabolic intermediates.1 Publication

Catalytic activityi

5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol + 6 reduced adrenodoxin + 6 H+ + 3 O2 = (25R)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestan-26-oate + 6 oxidized adrenodoxin + 4 H2O.1 Publication

Cofactori

hemeBy similarity

Enzyme regulationi

Activated by partially methylated beta-cyclodextrin.1 Publication

Kineticsi

  1. KM=13.5 µM for vitamin D31 Publication
  2. KM=7.1 µM for 25-hydroxyvitamin D31 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi347 – 3471Iron (heme axial ligand)By similarity

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Monooxygenase, Oxidoreductase

    Keywords - Ligandi

    Heme, Iron, Metal-binding, NADP

    Enzyme and pathway databases

    BRENDAi1.14.13.159. 309.
    SABIO-RKC4B644.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vitamin D(3) 25-hydroxylase1 PublicationImported (EC:1.14.15.151 Publication)
    Alternative name(s):
    Cytochrome P450By similarity
    Gene namesi
    Name:vdhImported
    OrganismiPseudonocardia autotrophica (Amycolata autotrophica) (Nocardia autotrophica)
    Taxonomic identifieri2074 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaPseudonocardialesPseudonocardiaceaePseudonocardia

    Subcellular locationi

    • Cytoplasm By similarity

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi70 – 701T → R: Increases 25-hydroxylase activity 2.0-fold. Increases 25-hydroxylase activity 21.6-fold; when associated with V156L, E216M and E348R. 1 Publication
    Mutagenesisi156 – 1561V → L: Increases 25-hydroxylase activity 21.6-fold; when associated with T70R; E216M and E348R. 1 Publication
    Mutagenesisi156 – 1561V → S: Increases 25-hydroxylase activity 2.5-fold. 1 Publication
    Mutagenesisi216 – 2161E → A: Increases 25-hydroxylase activity 1.9-fold. 1 Publication
    Mutagenesisi216 – 2161E → M: Increases 25-hydroxylase activity 21.6-fold; when associated with T70R; V156L and E348R. 1 Publication
    Mutagenesisi384 – 3841E → R: Increases 25-hydroxylase activity 2.8-fold. Increases 25-hydroxylase activity 21.6-fold; when associated with T70R; V156L and E216M. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 403402Vitamin D(3) 25-hydroxylase1 PublicationPRO_0000383672Add
    BLAST

    Structurei

    Secondary structure

    1
    403
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 93Combined sources
    Beta strandi13 – 153Combined sources
    Helixi16 – 183Combined sources
    Helixi23 – 3210Combined sources
    Beta strandi34 – 407Combined sources
    Beta strandi43 – 486Combined sources
    Helixi51 – 588Combined sources
    Beta strandi63 – 653Combined sources
    Helixi67 – 704Combined sources
    Helixi73 – 753Combined sources
    Turni76 – 783Combined sources
    Helixi87 – 893Combined sources
    Helixi94 – 10310Combined sources
    Helixi104 – 1063Combined sources
    Helixi108 – 12821Combined sources
    Beta strandi131 – 1333Combined sources
    Helixi137 – 1404Combined sources
    Turni141 – 1444Combined sources
    Helixi145 – 15410Combined sources
    Helixi158 – 1603Combined sources
    Helixi161 – 17111Combined sources
    Turni177 – 1793Combined sources
    Helixi180 – 20021Combined sources
    Helixi206 – 2127Combined sources
    Turni218 – 2203Combined sources
    Helixi223 – 23715Combined sources
    Helixi239 – 25315Combined sources
    Helixi256 – 2649Combined sources
    Helixi266 – 2683Combined sources
    Helixi269 – 27911Combined sources
    Beta strandi289 – 2935Combined sources
    Beta strandi295 – 2973Combined sources
    Beta strandi300 – 3023Combined sources
    Beta strandi307 – 3115Combined sources
    Helixi312 – 3154Combined sources
    Turni319 – 3213Combined sources
    Beta strandi322 – 3243Combined sources
    Beta strandi338 – 3403Combined sources
    Helixi343 – 3453Combined sources
    Helixi350 – 36718Combined sources
    Beta strandi372 – 3754Combined sources
    Helixi377 – 3793Combined sources
    Beta strandi386 – 3883Combined sources
    Beta strandi395 – 3973Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3A4GX-ray1.75A1-403[»]
    3A4HX-ray3.06A1-403[»]
    3A4ZX-ray2.20A/B/C/D/E1-403[»]
    3A50X-ray2.05A/B/C/D/E1-403[»]
    3A51X-ray2.00A/B/C/D/E1-403[»]
    3VRMX-ray2.57A1-403[»]
    ProteinModelPortaliC4B644.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiC4B644.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the cytochrome P450 family.Sequence analysis

    Family and domain databases

    Gene3Di1.10.630.10. 1 hit.
    InterProiIPR001128. Cyt_P450.
    IPR002397. Cyt_P450_B.
    IPR017972. Cyt_P450_CS.
    [Graphical view]
    PfamiPF00067. p450. 1 hit.
    [Graphical view]
    PRINTSiPR00359. BP450.
    SUPFAMiSSF48264. SSF48264. 1 hit.
    PROSITEiPS00086. CYTOCHROME_P450. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    C4B644-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MALTTTGTEQ HDLFSGTFWQ NPHPAYAALR AEDPVRKLAL PDGPVWLLTR
    60 70 80 90 100
    YADVREAFVD PRLSKDWRHT LPEDQRADMP ATPTPMMILM DPPDHTRLRK
    110 120 130 140 150
    LVGRSFTVRR MNELEPRITE IADGLLAGLP TDGPVDLMRE YAFQIPVQVI
    160 170 180 190 200
    CELLGVPAED RDDFSAWSSV LVDDSPADDK NAAMGKLHGY LSDLLERKRT
    210 220 230 240 250
    EPDDALLSSL LAVSDEDGDR LSQEELVAMA MLLLIAGHET TVNLIGNGVL
    260 270 280 290 300
    ALLTHPDQRK LLAEDPSLIS SAVEEFLRFD SPVSQAPIRF TAEDVTYSGV
    310 320 330 340 350
    TIPAGEMVML GLAAANRDAD WMPEPDRLDI TRDASGGVFF GHGIHFCLGA
    360 370 380 390 400
    QLARLEGRVA IGRLFADRPE LALAVGLDEL VYRESTLVRG LSRMPVTMGP

    RSA
    Length:403
    Mass (Da):44,369
    Last modified:July 7, 2009 - v1
    Checksum:i5984C6AE5AA1C756
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti4 – 63Missing AA sequence (PubMed:19450562).Curated
    Sequence conflicti17 – 171T → F AA sequence (PubMed:19450562).Curated
    Sequence conflicti23 – 253HPA → QPP AA sequence (PubMed:19450562).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB456955 Genomic DNA. Translation: BAH58688.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB456955 Genomic DNA. Translation: BAH58688.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3A4GX-ray1.75A1-403[»]
    3A4HX-ray3.06A1-403[»]
    3A4ZX-ray2.20A/B/C/D/E1-403[»]
    3A50X-ray2.05A/B/C/D/E1-403[»]
    3A51X-ray2.00A/B/C/D/E1-403[»]
    3VRMX-ray2.57A1-403[»]
    ProteinModelPortaliC4B644.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi1.14.13.159. 309.
    SABIO-RKC4B644.

    Miscellaneous databases

    EvolutionaryTraceiC4B644.

    Family and domain databases

    Gene3Di1.10.630.10. 1 hit.
    InterProiIPR001128. Cyt_P450.
    IPR002397. Cyt_P450_B.
    IPR017972. Cyt_P450_CS.
    [Graphical view]
    PfamiPF00067. p450. 1 hit.
    [Graphical view]
    PRINTSiPR00359. BP450.
    SUPFAMiSSF48264. SSF48264. 1 hit.
    PROSITEiPS00086. CYTOCHROME_P450. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Purification, characterization, and directed evolution study of a vitamin D3 hydroxylase from Pseudonocardia autotrophica."
      Fujii Y., Kabumoto H., Nishimura K., Fujii T., Yanai S., Takeda K., Tamura N., Arisawa A., Tamura T.
      Biochem. Biophys. Res. Commun. 385:170-175(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-28 AND 187-198, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF THR-70; VAL-156; GLU-216 AND GLU-384.
      Strain: ATCC 19727 / DSM 535 / NBRC 12743.

    Entry informationi

    Entry nameiCPVDH_PSEAH
    AccessioniPrimary (citable) accession number: C4B644
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 22, 2009
    Last sequence update: July 7, 2009
    Last modified: June 8, 2016
    This is version 33 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.