4XO7

Crystal structure of human 3-alpha hydroxysteroid dehydrogenase type 3 in complex with NADP+, 5alpha-androstan-3,17-dione and (3beta, 5alpha)-3-hydroxyandrostan-17-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Human 3 alpha-hydroxysteroid dehydrogenase type 3: structural clues of 5 alpha-DHT reverse binding and enzyme down-regulation decreasing MCF7 cell growth.

Zhang, B.Hu, X.J.Wang, X.Q.Theriault, J.F.Zhu, D.W.Shang, P.Labrie, F.Lin, S.X.

(2016) Biochem J 473: 1037-1046

  • DOI: https://doi.org/10.1042/BCJ20160083
  • Primary Citation of Related Structures:  
    4XO6, 4XO7

  • PubMed Abstract: 

    Human 3α-HSD3 (3α-hydroxysteroid dehydrogenase type 3) plays an essential role in the inactivation of the most potent androgen 5α-DHT (5α-dihydrotestosterone). The present study attempts to obtain the important structure of 3α-HSD3 in complex with 5α-DHT and to investigate the role of 3α-HSD3 in breast cancer cells. We report the crystal structure of human 3α-HSD3·NADP(+)·A-dione (5α-androstane-3,17-dione)/epi-ADT (epiandrosterone) complex, which was obtained by co-crystallization with 5α-DHT in the presence of NADP(+) Although 5α-DHT was introduced during the crystallization, oxidoreduction of 5α-DHT occurred. The locations of A-dione and epi-ADT were identified in the steroid-binding sites of two 3α-HSD3 molecules per crystal asymmetric unit. An overlay showed that A-dione and epi-ADT were oriented upside-down and flipped relative to each other, providing structural clues for 5α-DHT reverse binding in the enzyme with the generation of different products. Moreover, we report the crystal structure of the 3α-HSD3·NADP(+)·4-dione (4-androstene-3,17-dione) complex. When a specific siRNA (100 nM) was used to suppress 3α-HSD3 expression without interfering with 3α-HSD4, which shares a highly homologous active site, the 5α-DHT concentration increased, whereas MCF7 cell growth was suppressed. The present study provides structural clues for 5α-DHT reverse binding within 3α-HSD3, and demonstrates for the first time that down-regulation of 3α-HSD3 decreases MCF7 breast cancer cell growth.


  • Organizational Affiliation

    Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Quebec Research Center (CHUL, CHU) and Laval University, Québec City, Québec, G1V4G2, Canada Key Laboratory for Space Bioscience and Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member C2
A, B
323Homo sapiensMutation(s): 0 
Gene Names: AKR1C2DDH2
EC: 1.3.1.20 (PDB Primary Data), 1.1.1.357 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.209 (UniProt), 1 (UniProt), 1.1.1.62 (UniProt), 1.1.1.112 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P52895 (Homo sapiens)
Explore P52895 
Go to UniProtKB:  P52895
PHAROS:  P52895
GTEx:  ENSG00000151632 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52895
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
ASD
Query on ASD

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
4-ANDROSTENE-3-17-DIONE
C19 H26 O2
AEMFNILZOJDQLW-QAGGRKNESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.9α = 90
b = 86.65β = 106.25
c = 76.99γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2016-04-20
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description