3QWI

Crystal structure of a 17beta-hydroxysteroid dehydrogenase (holo form) from fungus Cochliobolus lunatus in complex with NADPH and coumestrol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural studies on the flavonoid inhibition of a fungal 17Beta-Hydroxysteroid dehydrogenase

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

(2012) Biochem.J. 441: 151-160

  • DOI: 10.1042/BJ20110567
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 17β-HSD (17β-hydroxysteroid dehydrogenase) from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) is a NADP(H)-dependent enzyme that preferentially catalyses the interconversion of inactive 17-oxo-steroids and their active 17β-hydroxy count ...

    The 17β-HSD (17β-hydroxysteroid dehydrogenase) from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) is a NADP(H)-dependent enzyme that preferentially catalyses the interconversion of inactive 17-oxo-steroids and their active 17β-hydroxy counterparts. 17β-HSDcl belongs to the SDR (short-chain dehydrogenase/reductase) superfamily. It is currently the only fungal 17β-HSD member that has been described and represents one of the model enzymes of the cP1 classical subfamily of NADPH-dependent SDR enzymes. A thorough crystallographic analysis has been performed to better understand the structural aspects of this subfamily and provide insights into the evolution of the HSD enzymes. The crystal structures of the 17β-HSDcl apo, holo and coumestrol-inhibited ternary complex, and the active-site Y167F mutant reveal subtle conformational differences in the substrate-binding loop that probably modulate the catalytic activity of 17β-HSDcl. Coumestrol, a plant-derived non-steroidal compound with oestrogenic activity, inhibits 17β-HSDcl [IC50 2.8 μM; at 100 μM substrate (4-oestrene-3,17-dione)] by occupying the putative steroid-binding site. In addition to an extensive hydrogen-bonding network, coumestrol binding is stabilized further by π-π stacking interactions with Tyr212. A stopped-flow kinetic experiment clearly showed the coenzyme dissociation as the slowest step of the reaction and, in addition to the low steroid solubility, it prevents the accumulation of enzyme-coenzyme-steroid ternary complexes.


    Organizational Affiliation

    Istituto di Cristallografia - UOS Trieste, Consiglio Nazionale delle Ricerche, Area Science Park-Basovizza, S.S. 14 km 163.5, I-34149 Trieste, Italy. alberto.cassetta@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, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CUE
Query on CUE

Download SDF File 
Download CCD File 
A, B, D
Coumestrol
3,9-dihydroxy-6H-[1]benzofuro[3,2-c]chromen-6-one
C15 H8 O5
ZZIALNLLNHEQPJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CUEIC50: 2800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.410α = 90.00
b = 116.810β = 103.14
c = 70.430γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Non-polymer description
  • Version 1.2: 2017-11-08
    Type: Refinement description