1MRQ

Crystal structure of human 20alpha-HSD in ternary complex with NADP and 20alpha-hydroxy-progesterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.194 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.190 (DCC) 

Starting Model: experimental
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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 1.4 of the entry. See complete history


Literature

Human 20alpha-hydroxysteroid dehydrogenase: crystallographic and site-directed mutagenesis studies lead to the identification of an alternative binding site for C21-steroids.

Couture, J.F.Legrand, P.Cantin, L.Luu-The, V.Labrie, F.Breton, R.

(2003) J Mol Biol 331: 593-604

  • DOI: https://doi.org/10.1016/s0022-2836(03)00762-9
  • Primary Citation of Related Structures:  
    1MRQ

  • PubMed Abstract: 

    Human 20alpha-hydroxysteroid dehydrogenase (h20alpha-HSD; AKR1C1) catalyzes the transformation of progesterone (Prog) into 20alpha-hydroxy-progesterone (20alpha-OHProg). Although h20alpha-HSD shares 98% sequence identity with human type 3 3alpha-HSD (h3alpha-HSD3, AKR1C2), these two enzymes differ greatly in their activities. In order to explain these differences, we have solved the crystal structure of h20alpha-HSD in a ternary complex with NADP(+) and 20alpha-OHProg at 1.59A resolution. The steroid is stabilized by numerous hydrophobic interactions and a hydrogen bond between its O20 and the N(epsilon ) atom of His222. This new interaction prevents the formation of a hydrogen bond with the cofactor, as seen in h3alpha-HSD3 ternary complexes. By combining structural, direct mutagenesis and kinetic studies, we found that the H(222)I substitution decreases the K(m) value for the cofactor 95-fold. With these results, we hypothesize that the rotation of the lateral chain of His222 could be a mediating step between the transformation of Prog and the release of the cofactor. Moreover, crystal structure analysis and direct mutagenesis experiments lead us to identify a new residue involved in the binding of Prog. Indeed, the R(304)L substitution leads to a 65-fold decrease in the K(m) value for Prog reduction. We thus propose that Prog is maintained in a new steroid-binding site composed mainly of residues found in the carboxy-terminal region of the protein.


  • Organizational Affiliation

    Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL) 2705 boul. Laurier, Ste-Foy, Qc., Canada G1V 4G2.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member C1323Homo sapiensMutation(s): 0 
EC: 1.1.1.149 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.209 (UniProt), 1.3.1.20 (UniProt), 1.1.1.51 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (UniProt), 1.1.1 (UniProt), 1.1.1.210 (UniProt), 1.1.1.112 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q04828 (Homo sapiens)
Explore Q04828 
Go to UniProtKB:  Q04828
PHAROS:  Q04828
GTEx:  ENSG00000187134 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04828
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.194 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.190 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.65α = 90
b = 83.54β = 90
c = 100.68γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
AMoREphasing
REFMACrefinement
XDSdata scaling

Structure Validation

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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: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description