8EG3

Structure of human placental steroid (estrone/DHEA) sulfatase at 2.0 angstrom resolution

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMmpstruc

  • Deposited: 2022-09-10 Released: 2022-12-07 
  • Deposition Author(s): Ghosh, D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1P49


Literature

Structure of human placental steroid sulfatase at 2.0 angstrom resolution: Catalysis, quaternary association, and a secondary ligand site.

Ghosh, D.

(2022) J Steroid Biochem Mol Biol 227: 106228-106228

  • DOI: https://doi.org/10.1016/j.jsbmb.2022.106228
  • Primary Citation of Related Structures:  
    8EG3

  • PubMed Abstract: 

    Human placental estrone (E1)/dehydroepiandrosterone (DHEA) sulfatase (human placental steroid sulfatase; hSTS) is an integral membrane protein of the endoplasmic reticulum. This Ca 2+ -dependent enzyme catalyzes the hydrolysis of sulfate esters of E1 and DHEA to yield the respective unconjugated steroids, which then act as precursors for the biosynthesis of 17β-estradiol (E2) and dihydrotestosterone (DHT), respectively, the most potent forms of estrogens and androgens. hSTS is a key enzyme for the local production of E2 and DHT in the breast and the prostate. The enzyme is known to be responsible for maintaining high levels of estrogens in the breast tumor cells. The crystal structure of hSTS purified from human placenta has previously been reported at 2.6 Å resolution. Here we present the structure of hSTS determined at the superior 2.0 Å resolution bringing new clarity to the atomic architecture of the active site. The molecular basis of catalysis and steroid-protein interaction are revisited in light of the new data. We also reexamine the enzyme's quaternary association and its implication on the membrane integration. A secondary ligand binding pocket at the intermolecular interface and adjacent to the active site access channel, buried into the gill of the mushroom-shaped molecule, has been identified. Its role as well as that of a phosphate ion bound to an exposed histidine side chain are examined from the structure-function perspective. Higher resolution data also aids in the tracing of an important loop missing in the previous structure.


  • Organizational Affiliation

    Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA. Electronic address: ghoshd@upstate.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steryl-sulfatase583Homo sapiensMutation(s): 0 
EC: 3.1.6.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08842 (Homo sapiens)
Explore P08842 
Go to UniProtKB:  P08842
PHAROS:  P08842
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08842
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P08842-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG (Subject of Investigation/LOI)
Query on BOG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALS
Query on ALS
A
L-PEPTIDE LINKINGC3 H7 N O7 SALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.19α = 90
b = 117.19β = 90
c = 102.68γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-12-07 
  • Deposition Author(s): Ghosh, D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States62794

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description