5X7E

Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Literature

Production of an active form of vitamin D2 by genetically engineered CYP105A1

Yasuda, K.Yogo, Y.Sugimoto, H.Mano, H.Takita, T.Ohta, M.Kamakura, M.Ikushiro, S.Yasukawa, K.Shiro, Y.Sakaki, T.

(2017) Biochem Biophys Res Commun 486: 336-341

  • DOI: https://doi.org/10.1016/j.bbrc.2017.03.040
  • Primary Citation of Related Structures:  
    5X7E

  • PubMed Abstract: 

    Our previous studies revealed that CYP105A1 can convert vitamin D 3 (VD3) to its active form, 1α,25-dihydroxyvitamin D 3 (1,25D3). Site-directed mutagenesis of CYP105A1 based on its crystal structure dramatically enhanced its activity; the activity of double variants R73A/R84A and R73A/R84V was more than 100-fold higher than that of the wild type of CYP105A1. In contrast, these variants had a low ability to convert vitamin D 2 (VD2) to 1α,25-dihydroxyvitamin D 2 (1,25D2), whereas they catalyzed the sequential hydroxylation at positions C25 and C26 to produce 25,26D2. A comparison of the docking models of 25D2 and 25D3 into the substrate-binding pocket of R73A/R84A suggests that the side chain of the Met239 inhibits the binding of 25D2 for 1α-hydroxylation. Therefore, the Met239 residue of R73A/R84A was substituted for Ala. As expected, the triple variant R73A/R84A/M239A showed a 22-fold higher 1α-hydroxylation activity towards 25D2. To the best of our knowledge, this is the first report on the generation of microbial cytochrome P450 that converts VD2 to 1,25D2 via 25D2.


  • Organizational Affiliation

    Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 dihydroxylase412Streptomyces griseolusMutation(s): 2 
Gene Names: cyp105A1suaC
EC: 1.14.15
UniProt
Find proteins for P18326 (Streptomyces griseolus)
Explore P18326 
Go to UniProtKB:  P18326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18326
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
7ZU
Query on 7ZU

Download Ideal Coordinates CCD File 
C [auth A](1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(E,2R,5S)-5,6-dimethyl-6-oxidanyl-hept-3-en-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydr o-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
C28 H44 O3
ZGLHBRQAEXKACO-XJRQOBMKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.409α = 90
b = 53.36β = 90
c = 139.436γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary