4L1X

Crystal Structuer of Human 3-alpha Hydroxysteroid Dehydrogenase Type 3 V54L Mutant in Complex with NADP+ and Progesterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.183 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view detailsBest fitted STRClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Human 3-alpha hydroxysteroid dehydrogenase type 3 (3 alpha-HSD3): The V54L mutation restricting the steroid alternative binding and enhancing the 20 alpha-HSD activity

Zhang, B.Zhu, D.-W.Hu, X.-J.Zhou, M.Shang, P.Lin, S.-X.

(2014) J Steroid Biochem Mol Biol 141: 135-143

  • DOI: https://doi.org/10.1016/j.jsbmb.2014.01.003
  • Primary Citation of Related Structures:  
    4L1W, 4L1X

  • PubMed Abstract: 

    Human 3-alpha hydroxysteroid dehydrogenase type 3 (3α-HSD3) has an essential role in the inactivation of 5α-dihydrotestosterone (DHT). Notably, human 3α-HSD3 shares 97.8% sequence identity with human 20-alpha hydroxysteroid dehydrogenase (20α-HSD) and there is only one amino acid difference (residue 54) that is located in their steroid binding pockets. However, 20α-HSD displays a distinctive ability in transforming progesterone to 20α-hydroxy-progesterone (20α-OHProg). In this study, to understand the role of residue 54 in the steroid binding and discrimination, the V54L mutation in human 3α-HSD3 has been created. We have solved two crystal structures of the 3α-HSD3·NADP(+)·Progesterone complex and the 3α-HSD3 V54L·NADP(+)·progesterone complex. Interestingly, progesterone adopts two different binding modes to form complexes within the wild type enzyme, with one binding mode similar to the orientation of a bile acid (ursodeoxycholate) in the reported ternary complex of human 3α-HSD3·NADP(+)·ursodeoxycholate and the other binding mode resembling the orientation of 20α-OHProg in the ternary complex of human 20α-HSD·NADP(+)·20α-OHProg. However, the V54L mutation directly restricts the steroid binding modes to a unique one, which resembles the orientation of 20α-OHProg within human 20α-HSD. Furthermore, the kinetic study has been carried out. The results show that the V54L mutation significantly decreases the 3α-HSD activity for the reduction of DHT, while this mutation enhances the 20α-HSD activity to convert progesterone.


  • Organizational Affiliation

    Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire (CHU) de Quebec Research Center (CHUL) and Laval University, Québec City, Québec G1V4G2, Canada; Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, PR 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
325Homo sapiensMutation(s): 1 
Gene Names: AKR1C2
EC: 1.3.1.20 (PDB Primary Data), 1.1.1.213 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.209 (UniProt), 1 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.183 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.14α = 90
b = 87.1β = 106.31
c = 76.87γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view detailsBest fitted STRClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description