6MNE

CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH ESTRONE AND NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of human 17 beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NADP+reveal the mechanism of substrate inhibition.

Li, T.Stephen, P.Zhu, D.W.Shi, R.Lin, S.X.

(2019) Febs J. 286: 2155-2166

  • DOI: 10.1111/febs.14784
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyses the last step in estrogen activation and is thus involved in estrogen-dependent diseases (EDDs). Unlike other 17β-HSD members, 17β-HSD1 undergoes a significant substrate-induced inhib ...

    Human 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyses the last step in estrogen activation and is thus involved in estrogen-dependent diseases (EDDs). Unlike other 17β-HSD members, 17β-HSD1 undergoes a significant substrate-induced inhibition that we have previously reported. Here we solved the binary and ternary crystal structures of 17β-HSD1 in complex with estrone (E1) and cofactor analog NADP + , demonstrating critical enzyme-substrate-cofactor interactions. These complexes revealed a reversely bound E1 in 17β-HSD1 that provides the basis of the substrate inhibition, never demonstrated in estradiol complexes. Structural analysis showed that His 221 is the key residue responsible for the reorganization and stabilization of the reversely bound E1, leading to the formation of a dead-end complex, which exists widely in NADP(H)-preferred enzymes for the regulation of their enzymatic activity. Further, a new inhibitor is proposed that may inhibit 17β-HSD1 through the formation of a dead-end complex. This finding indicates a simple mechanism of enzyme regulation in the physiological background and introduces a pioneer inhibitor of 17β-HSD1 based on the dead-end inhibition model for efficiently targeting EDDs. DATABASES: Coordinates and structure factors of 17β-HSD1-E1 and 17β-HSD1-E1-NADP + have been deposited in the Protein Data Bank with accession code 6MNC and 6MNE respectively. ENZYMES: 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1) EC 1.1.1.62.


    Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Republic of Korea. Sunglee@chosun.ac.kr.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Republic of Korea.,Department of Chemistry, University of Washington, 4000 15th Ave NE, Bagley Hall, Seattle, WA, 98195-1700, USA.,Axe Molecular Endocrinology and Nephrology, CHU de Québec Research Center, Department of Molecular Medicine, Laval University, Québec, Canada.,Department of Environmental Engineering, Chosun University, Gwangju, 61452, Republic of Korea.,Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA.,Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Sanofi-Aventis Pharma Deutschland GmbH, Frankfurt am Main, Germany.,Molecular Biology Institute, University of California, Los Angeles, CA, USA.,KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.,Département de Biochimie, de Microbiologie et de Bio-Informatique, IBIS et PROTEO, Université Laval, Pavillon Charles-Eugène Marchand, Québec, Canada.,Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estradiol 17-beta-dehydrogenase 1
A, B
328Homo sapiensMutation(s): 0 
Gene Names: HSD17B1 (E17KSR, EDH17B1, EDH17B2, EDHB17, SDR28C1)
EC: 1.1.1.62
Find proteins for P14061 (Homo sapiens)
Go to Gene View: HSD17B1
Go to UniProtKB:  P14061
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
J3Z
Query on J3Z

Download SDF File 
Download CCD File 
A, B
(9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one
Estrone
C18 H22 O2
DNXHEGUUPJUMQT-CBZIJGRNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.780α = 90.00
b = 108.240β = 90.00
c = 117.670γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-10-01 
  • Released Date: 2019-04-03 
  • Deposition Author(s): Li, T., Lin, S.X.

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection, Database references