4FJ2

Crystal structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and biochanin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for inhibition of 17 beta-hydroxysteroid dehydrogenases by phytoestrogens: The case of fungal 17 beta-HSDcl.

Cassetta, A.Stojan, J.Krastanova, I.Kristan, K.Brunskole Svegelj, M.Lamba, D.Rizner, T.L.

(2017) J. Steroid Biochem. Mol. Biol. 171: 80-93

  • DOI: 10.1016/j.jsbmb.2017.02.020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phytoestrogens are plant-derived compounds that functionally and structurally mimic mammalian estrogens. Phytoestrogens have broad inhibitory activities toward several steroidogenic enzymes, such as the 17β-hydroxysteroid dehydrogenases (17β-HSDs), w ...

    Phytoestrogens are plant-derived compounds that functionally and structurally mimic mammalian estrogens. Phytoestrogens have broad inhibitory activities toward several steroidogenic enzymes, such as the 17β-hydroxysteroid dehydrogenases (17β-HSDs), which modulate the biological potency of androgens and estrogens in mammals. However, to date, no crystallographic data are available to explain phytoestrogens binding to mammalian 17β-HSDs. NADP(H)-dependent 17β-HSD from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) has been the subject of extensive biochemical, kinetic and quantitative structure-activity relationship studies that have shown that the flavonols are the most potent inhibitors. In the present study, we investigated the structure-activity relationships of the ternary complexes between the holo form of 17β-HSDcl and the flavonols kaempferol and 3,7-dihydroxyflavone, in comparison with the isoflavones genistein and biochanin A. Crystallographic data are accompanied by kinetic analysis of the inhibition mechanisms for six flavonols (3-hydroxyflavone, 3,7-dihydroxyflavone, kaempferol, quercetin, fisetin, myricetin), one flavanone (naringenin), one flavone (luteolin), and two isoflavones (genistein, biochanin A). The kinetics analysis shows that the degree of hydroxylation of ring B significantly influences the overall inhibitory efficacy of the flavonols. A distinct binding mode defines the interactions between 17β-HSDcl and the flavones and isoflavones. Moreover, the complex with biochanin A reveals an unusual binding mode that appears to account for its greater inhibition of 17β-HSDcl with respect to genistein. Overall, these data provide a blueprint for identification of the distinct molecular determinants that underpin 17β-HSD inhibition by phytoestrogens.


    Organizational Affiliation

    Istituto di Cristallografia, UOS Trieste, Consiglio Nazionale delle Ricerche, S. S. 14-Km 163.5, I-34149, Trieste, Italy. Electronic address: alberto.cassetta@ts.ic.cnr.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
17beta-hydroxysteroid dehydrogenase
A, B, C, D
270Cochliobolus lunatusMutation(s): 0 
Gene Names: 17HSDcl
Find proteins for O93874 (Cochliobolus lunatus)
Go to UniProtKB:  O93874
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
QSO
Query on QSO

Download SDF File 
Download CCD File 
B, D
5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one
Biochanin A
C16 H12 O5
WUADCCWRTIWANL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.430α = 90.00
b = 115.280β = 102.93
c = 69.600γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XSCALEdata scaling
XRD1data collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Structure summary
  • Version 1.2: 2017-07-19
    Type: Database references