9KOQ | pdb_00009koq

Crystal structure of an Arylsulfatase from Enterococcus faecium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into manganese-dependent arylsulfatase from Enterococcus faecium and its catalytic promiscuity.

Guo, L.Dong, X.Hu, Z.Zeng, L.Jin, Z.Jiang, L.Dai, W.Ma, J.Chen, S.Huang, Y.

(2025) mBio 16: e0003125-e0003125

  • DOI: https://doi.org/10.1128/mbio.00031-25
  • Primary Citation of Related Structures:  
    9KOQ

  • PubMed Abstract: 

    Catalytic promiscuity, wherein enzymes catalyze multiple distinct reactions by stabilizing various transition states, is well documented in the alkaline phosphatase superfamily. In this study, we determined the crystal structure of an arylsulfatase from Enterococcus faecium (EfAS), revealing a homotetrameric assembly with a windmill-like architecture not observed in other known arylsulfatases or phosphonoester hydrolases. This quaternary structure is stabilized by hydrogen bonding, salt bridges, and hydrophobic interactions, while retaining full accessibility to the catalytic groove. Moreover, by incorporating a manganese ion in its active site, EfAS provides the first crystallographically confirmed example of a Mn² + -dependent arylsulfatase, addressing previous uncertainties regarding metal specificity. Functional assays and site-directed mutagenesis showed that EfAS hydrolyzes sulfates, phosphates, and phosphonates, indicating broad substrate specificity. Furthermore, high-performance liquid chromatography-mass spectrometry demonstrated that EfAS removes sulfate groups from key bioactive molecules, such as caerulein and estrone sulfate. Collectively, these findings establish EfAS as an atypical member of the alkaline phosphatase superfamily, featuring a distinct oligomeric organization and broad substrate scope, and suggest its potential role in modulating sulfation of bioactive compounds.IMPORTANCEThis work provides the first crystallographically confirmed Mn² + -dependent arylsulfatase, unveiling a unique "windmill-like" homotetrameric architecture and demonstrating catalytic promiscuity toward sulfates, phosphates, and phosphonates. These findings address longstanding uncertainties about metal specificity in arylsulfatases, highlight the structural and functional diversity of the alkaline phosphatase superfamily, and suggest new strategies for modulating the sulfation of bioactive molecules.


  • Organizational Affiliation
    • Shanghai Key Laboratory of Biliary Tract Disease Research, Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfatase
A, B
487Enterococcus faeciumMutation(s): 0 
Gene Names: pLG1-0063
EC: 3.1.6.1
UniProt
Find proteins for I3U6E8 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO))
Explore I3U6E8 
Go to UniProtKB:  I3U6E8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3U6E8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALS
Query on ALS
A, B
L-PEPTIDE LINKINGC3 H7 N O7 SALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.594α = 90
b = 151.594β = 90
c = 97.176γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171186

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Database references