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 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/s0022-2836(03)00762-9
  • Structures With Same Primary Citation

  • 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 ...

    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.


    Related Citations: 
    • Expression, crystallization and preliminary X-ray analysis of human and rabbit 20alpha-hydroxysteroid dehydrogenase in complex with NADP(H) and various steroid substrates
      Couture, J.F., Cantin, L., Legrand, P., Luu-The, V., Labrie, F., Breton, R.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 135

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldo-keto reductase family 1 member C1
A
323Homo sapiensMutation(s): 0 
Gene Names: AKR1C1DDHDDH1
EC: 1.1.1.149 (PDB Primary Data), 1.1.1 (UniProt), 1.1.1.112 (UniProt), 1.3.1.20 (UniProt)
Find proteins for Q04828 (Homo sapiens)
Go to UniProtKB:  Q04828
NIH Common Fund Data Resources
PHAROS  Q04828
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
STR
Query on STR

Download CCD File 
A
PROGESTERONE
C21 H30 O2
RJKFOVLPORLFTN-LEKSSAKUSA-N
 Ligand Interaction
BME
Query on BME

Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • 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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Entry History 

Deposition Data

Revision History 

  • 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