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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)DescriptionActionsGraphical viewLength
    Metal bindingi347Iron (heme axial ligand)By similarity1

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi70T → R: Increases 25-hydroxylase activity 2.0-fold. Increases 25-hydroxylase activity 21.6-fold; when associated with V156L, E216M and E348R. 1 Publication1
    Mutagenesisi156V → L: Increases 25-hydroxylase activity 21.6-fold; when associated with T70R; E216M and E348R. 1 Publication1
    Mutagenesisi156V → S: Increases 25-hydroxylase activity 2.5-fold. 1 Publication1
    Mutagenesisi216E → A: Increases 25-hydroxylase activity 1.9-fold. 1 Publication1
    Mutagenesisi216E → M: Increases 25-hydroxylase activity 21.6-fold; when associated with T70R; V156L and E348R. 1 Publication1
    Mutagenesisi384E → R: Increases 25-hydroxylase activity 2.8-fold. Increases 25-hydroxylase activity 21.6-fold; when associated with T70R; V156L and E216M. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00003836722 – 403Vitamin D(3) 25-hydroxylase1 PublicationAdd BLAST402

    Structurei

    Secondary structure

    1403
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi7 – 9Combined sources3
    Beta strandi13 – 15Combined sources3
    Helixi16 – 18Combined sources3
    Helixi23 – 32Combined sources10
    Beta strandi34 – 40Combined sources7
    Beta strandi43 – 48Combined sources6
    Helixi51 – 58Combined sources8
    Beta strandi63 – 65Combined sources3
    Helixi67 – 70Combined sources4
    Helixi73 – 75Combined sources3
    Turni76 – 78Combined sources3
    Helixi87 – 89Combined sources3
    Helixi94 – 103Combined sources10
    Helixi104 – 106Combined sources3
    Helixi108 – 128Combined sources21
    Beta strandi131 – 133Combined sources3
    Helixi137 – 140Combined sources4
    Turni141 – 144Combined sources4
    Helixi145 – 154Combined sources10
    Helixi158 – 160Combined sources3
    Helixi161 – 171Combined sources11
    Turni177 – 179Combined sources3
    Helixi180 – 200Combined sources21
    Helixi206 – 212Combined sources7
    Turni218 – 220Combined sources3
    Helixi223 – 237Combined sources15
    Helixi239 – 253Combined sources15
    Helixi256 – 264Combined sources9
    Helixi266 – 268Combined sources3
    Helixi269 – 279Combined sources11
    Beta strandi289 – 293Combined sources5
    Beta strandi295 – 297Combined sources3
    Beta strandi300 – 302Combined sources3
    Beta strandi307 – 311Combined sources5
    Helixi312 – 315Combined sources4
    Turni319 – 321Combined sources3
    Beta strandi322 – 324Combined sources3
    Beta strandi338 – 340Combined sources3
    Helixi343 – 345Combined sources3
    Helixi350 – 367Combined sources18
    Beta strandi372 – 375Combined sources4
    Helixi377 – 379Combined sources3
    Beta strandi386 – 388Combined sources3
    Beta strandi395 – 397Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiC4B644.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti4 – 6Missing AA sequence (PubMed:19450562).Curated3
    Sequence conflicti17T → F AA sequence (PubMed:19450562).Curated1
    Sequence conflicti23 – 25HPA → QPP AA sequence (PubMed:19450562).Curated3

    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
    PDB 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.
    SMRiC4B644.
    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...

    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: November 2, 2016
    This is version 35 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.