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Protein

Vitamin D3 dihydroxylase

Gene

cyp105A1

Organism
Streptomyces griseolus
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 D2.3 Publications

Catalytic activityi

Calcidiol + NADPH + O2 = calcitriol + NADP+ + H2O.3 Publications
Calciol + O2 + [reduced NADPH--hemoprotein reductase] = calcidiol + [oxidized NADPH--hemoprotein reductase] + H2O.3 Publications

Cofactori

heme3 Publications

Kineticsi

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.1 Publication

  1. KM=0.54 µM for vitamin D3 (at pH 7.4 and 30 degrees Celsius)1 Publication
  2. KM=0.59 µM for vitamin D2 (at pH 7.4 and 30 degrees Celsius)1 Publication
  3. KM=0.91 µM for 25-hydroxyvitamin D3 (1-alpha-hydroxylation)(at pH 7.4 and 30 degrees Celsius)1 Publication
  4. KM=4.4 µM for 25-hydroxyvitamin D3 (1-alpha-hydroxylation)1 Publication
  5. KM=5 µM for 25-hydroxyvitamin D3 (1-alpha-hydroxylation)1 Publication
  6. KM=9.4 µM for 1-alpha-hydroxyvitamin D3 (25-alpha-hydroxylation)1 Publication
  7. KM=10.1 µM for 1-alpha-hydroxyvitamin D3 (25-alpha-hydroxylation)1 Publication
  1. Vmax=8.4 µmol/min/mg enzyme with 25-hydroxyvitamin D3 as substrate (1-alpha-hydroxylation)1 Publication
  2. Vmax=3.8 µmol/min/mg enzyme with as 1-alpha-hydroxyvitamin D3 substrate (25-alpha-hydroxylation)1 Publication
  3. Vmax=3.6 mmol/min/mg enzyme with 25-hydroxyvitamin D3 as substrate (1-alpha-hydroxylation)(at pH 7.4 and 30 degrees Celsius)1 Publication
  4. Vmax=16 mmol/min/mg enzyme with vitamin D3 as substrate (at pH 7.4 and 30 degrees Celsius)1 Publication
  5. Vmax=84 mmol/min/mg enzyme with vitamin D2 as substrate (at pH 7.4 and 30 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei81 – 811Vitamin D31 Publication
Binding sitei103 – 1031Heme1 Publication
Binding sitei107 – 1071Heme1 Publication
Binding sitei193 – 1931Vitamin D32 Publications
Binding sitei236 – 2361Vitamin D31 Publication
Binding sitei293 – 2931Vitamin D3; via carbonyl oxygen2 Publications
Binding sitei297 – 2971Heme1 Publication
Binding sitei353 – 3531Heme1 Publication
Metal bindingi355 – 3551Iron (heme axial ligand)1 Publication

GO - Molecular functioni

GO - Biological processi

  • vitamin D3 metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Monooxygenase, Oxidoreductase

Keywords - Ligandi

Heme, Iron, Metal-binding, NADP

Names & Taxonomyi

Protein namesi
Recommended name:
Vitamin D3 dihydroxylaseCurated (EC:1.14.13.133 Publications, EC:1.14.14.243 Publications)
Alternative name(s):
CYP105A11 Publication
Cytochrome P450-CVA11 Publication
Cytochrome P450-SU11 Publication
Vitamin D3 hydroxylase1 Publication
Short name:
VD3 hydroxylase1 Publication
Gene namesi
Name:cyp105A11 Publication
Synonyms:suaC1 Publication
OrganismiStreptomyces griseolus
Taxonomic identifieri1909 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi73 – 731R → A, F, L or 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. 2 Publications
Mutagenesisi84 – 841R → A, Q, L or 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. 1 Publication
Mutagenesisi84 – 841R → 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. 1 Publication
Mutagenesisi88 – 881V → A: Decrease of the hydroxylase activity for both 25-hydroxyivitamin D3 and 1-alpha-hydroxyvitamin D3. 1 Publication
Mutagenesisi180 – 1801L → A: Decrease of the hydroxylase activity for both 25-hydroxyvitamin D3 and 1-alpha-hydroxyvitamin D3. 1 Publication
Mutagenesisi181 – 1811V → A: Decrease of the hydroxylase activity for both 25-hydroxyvitamin D3 and 1-alpha-hydroxyvitamin D3. 1 Publication
Mutagenesisi193 – 1931R → A, Q or K: Decrease of the hydroxylase activity. 1 Publication
Mutagenesisi293 – 2931I → A: Slight increase of the hydroxylase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 406405Vitamin D3 dihydroxylasePRO_0000052213Add
BLAST

Expressioni

Inductioni

By herbicides.1 Publication

Structurei

Secondary structure

1
406
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 173Combined sources
Helixi28 – 358Combined sources
Beta strandi36 – 449Combined sources
Beta strandi50 – 545Combined sources
Helixi57 – 648Combined sources
Helixi83 – 853Combined sources
Turni88 – 903Combined sources
Helixi95 – 973Combined sources
Helixi102 – 1076Combined sources
Turni108 – 1103Combined sources
Helixi111 – 1144Combined sources
Helixi116 – 14025Combined sources
Beta strandi142 – 1454Combined sources
Helixi146 – 1494Combined sources
Turni150 – 1523Combined sources
Helixi153 – 16311Combined sources
Helixi167 – 1693Combined sources
Helixi170 – 18213Combined sources
Helixi186 – 20924Combined sources
Helixi215 – 2217Combined sources
Turni222 – 2276Combined sources
Helixi231 – 26131Combined sources
Helixi264 – 2729Combined sources
Helixi274 – 2763Combined sources
Helixi277 – 28812Combined sources
Helixi292 – 2943Combined sources
Beta strandi296 – 3016Combined sources
Beta strandi303 – 3053Combined sources
Beta strandi308 – 3103Combined sources
Beta strandi315 – 3184Combined sources
Helixi320 – 3234Combined sources
Turni327 – 3293Combined sources
Beta strandi330 – 3323Combined sources
Helixi358 – 37518Combined sources
Beta strandi380 – 3834Combined sources
Helixi385 – 3873Combined sources
Beta strandi398 – 4003Combined sources
Beta strandi403 – 4053Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZBXX-ray1.50A1-406[»]
2ZBYX-ray1.60A1-406[»]
2ZBZX-ray1.90A1-406[»]
3CV8X-ray2.00A1-406[»]
3CV9X-ray1.70A1-406[»]
ProteinModelPortaliP18326.
SMRiP18326. Positions 4-406.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP18326.

Family & Domainsi

Sequence similaritiesi

Belongs to the cytochrome P450 family.Curated

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.
PR00385. P450.
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.

P18326-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDTATTPQT TDAPAFPSNR SCPYQLPDGY AQLRDTPGPL HRVTLYDGRQ
60 70 80 90 100
AWVVTKHEAA RKLLGDPRLS SNRTDDNFPA TSPRFEAVRE SPQAFIGLDP
110 120 130 140 150
PEHGTRRRMT ISEFTVKRIK GMRPEVEEVV HGFLDEMLAA GPTADLVSQF
160 170 180 190 200
ALPVPSMVIC RLLGVPYADH EFFQDASKRL VQSTDAQSAL TARNDLAGYL
210 220 230 240 250
DGLITQFQTE PGAGLVGALV ADQLANGEID REELISTAML LLIAGHETTA
260 270 280 290 300
SMTSLSVITL LDHPEQYAAL RADRSLVPGA VEELLRYLAI ADIAGGRVAT
310 320 330 340 350
ADIEVEGHLI RAGEGVIVVN SIANRDGTVY EDPDALDIHR SARHHLAFGF
360 370 380 390 400
GVHQCLGQNL ARLELEVILN ALMDRVPTLR LAVPVEQLVL RPGTTIQGVN

ELPVTW
Length:406
Mass (Da):44,212
Last modified:January 23, 2007 - v2
Checksum:iB41CDD7B9BC56191
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M32238 Genomic DNA. Translation: AAA26823.1.
PIRiA35401.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M32238 Genomic DNA. Translation: AAA26823.1.
PIRiA35401.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZBXX-ray1.50A1-406[»]
2ZBYX-ray1.60A1-406[»]
2ZBZX-ray1.90A1-406[»]
3CV8X-ray2.00A1-406[»]
3CV9X-ray1.70A1-406[»]
ProteinModelPortaliP18326.
SMRiP18326. Positions 4-406.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP18326.

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.
PR00385. P450.
SUPFAMiSSF48264. SSF48264. 1 hit.
PROSITEiPS00086. CYTOCHROME_P450. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genes for two herbicide-inducible cytochromes P-450 from Streptomyces griseolus."
    Omer C.A., Lenstra R., Litle P.J., Dean C., Tepperman J.M., Leto K.J., Romesser J.A., O'Keefe D.P.
    J. Bacteriol. 172:3335-3345(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-32, INDUCTION.
    Strain: ATCC 11796 / DSM 40854.
  2. "Conversion of vitamin D3 to 1alpha,25-dihydroxyvitamin D3 by Streptomyces griseolus cytochrome P450SU-1."
    Sawada N., Sakaki T., Yoneda S., Kusudo T., Shinkyo R., Ohta M., Inouye K.
    Biochem. Biophys. Res. Commun. 320:156-164(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, COFACTOR, SUBSTRATE SPECIFICITY.
  3. "Crystal structure of CYP105A1 (P450SU-1) in complex with 1alpha,25-dihydroxyvitamin D3."
    Sugimoto H., Shinkyo R., Hayashi K., Yoneda S., Yamada M., Kamakura M., Ikushiro S., Shiro Y., Sakaki T.
    Biochemistry 47:4017-4027(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: 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, COFACTOR.
  4. "Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1."
    Hayashi K., Sugimoto H., Shinkyo R., Yamada M., Ikeda S., Ikushiro S., Kamakura M., Shiro Y., Sakaki T.
    Biochemistry 47:11964-11972(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: 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, COFACTOR.

Entry informationi

Entry nameiCPXE_STRGO
AccessioniPrimary (citable) accession number: P18326
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 87 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.1 Publication
The hydrophobicity and the volume of the side chain at position 84 are critical for the activity.1 Publication

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.