8QFQ

Ergothioneine dioxygenase, variant H147A, from Thermocatellispora tengchongensis in complex with manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Enzyme-Catalyzed Oxidative Degradation of Ergothioneine.

Nalivaiko, E.Y.Vasseur, C.M.Seebeck, F.P.

(2024) Angew Chem Int Ed Engl 63: e202318445-e202318445

  • DOI: https://doi.org/10.1002/anie.202318445
  • Primary Citation of Related Structures:  
    8QFL, 8QFM, 8QFN, 8QFO, 8QFP, 8QFQ

  • PubMed Abstract: 

    Ergothioneine is a sulfur-containing metabolite that is produced by bacteria and fungi, and is absorbed by plants and animals as a micronutrient. Ergothioneine reacts with harmful oxidants, including singlet oxygen and hydrogen peroxide, and may therefore protect cells against oxidative stress. Herein we describe two enzymes from actinobacteria that cooperate in the specific oxidative degradation of ergothioneine. The first enzyme is an iron-dependent thiol dioxygenase that produces ergothioneine sulfinic acid. A crystal structure of ergothioneine dioxygenase from Thermocatellispora tengchongensis reveals many similarities with cysteine dioxygenases, suggesting that the two enzymes share a common mechanism. The second enzyme is a metal-dependent ergothioneine sulfinic acid desulfinase that produces Nα-trimethylhistidine and SO 2 . The discovery that certain actinobacteria contain the enzymatic machinery for O 2 -dependent biosynthesis and O 2 -dependent degradation of ergothioneine indicates that these organisms may actively manage their ergothioneine content.


  • Organizational Affiliation

    Department of Chemistry, University of Basel, Mattenstrasse 22, 4002, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine dioxygenase
A, B
184Thermocatellispora tengchongensisMutation(s): 1 
Gene Names: HNP84_002159
UniProt
Find proteins for A0A840P3H4 (Thermocatellispora tengchongensis)
Explore A0A840P3H4 
Go to UniProtKB:  A0A840P3H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A840P3H4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
D [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
M [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.419α = 90
b = 59.076β = 90
c = 134.629γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland182023

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Database references, Source and taxonomy