4X8E

Ergothioneine-biosynthetic sulfoxide synthase EgtB in complex with N,N,N-trimethyl-histidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Structure of the Sulfoxide Synthase EgtB from the Ergothioneine Biosynthetic Pathway.

Goncharenko, K.V.Vit, A.Blankenfeldt, W.Seebeck, F.P.

(2015) Angew.Chem.Int.Ed.Engl. 54: 2821-2824

  • DOI: 10.1002/anie.201410045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The non-heme iron enzyme EgtB catalyzes O2 -dependent C-S bond formation between γ-glutamyl cysteine and N-α-trimethyl histidine as the central step in ergothioneine biosynthesis. Both, the catalytic activity and the architecture of EgtB are distinct ...

    The non-heme iron enzyme EgtB catalyzes O2 -dependent C-S bond formation between γ-glutamyl cysteine and N-α-trimethyl histidine as the central step in ergothioneine biosynthesis. Both, the catalytic activity and the architecture of EgtB are distinct from known sulfur transferases or thiol dioxygenases. The crystal structure of EgtB from Mycobacterium thermoresistibile in complex with γ-glutamyl cysteine and N-α-trimethyl histidine reveals that the two substrates and three histidine residues serve as ligands in an octahedral iron binding site. This active site geometry is consistent with a catalytic mechanism in which C-S bond formation is initiated by an iron(III)-complexed thiyl radical attacking the imidazole ring of N-α-trimethyl histidine.


    Organizational Affiliation

    Department for Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel (Switzerland).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfoxide synthase EgtB
A, B
447Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)Mutation(s): 0 
Gene Names: egtB
EC: 1.14.99.50
Find proteins for G7CFI3 (Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Go to UniProtKB:  G7CFI3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AVJ
Query on AVJ

Download SDF File 
Download CCD File 
A, B
N,N,N-trimethyl-histidine
Hercynine
C9 H16 N3 O2
GPPYTCRVKHULJH-QMMMGPOBSA-O
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.241α = 90.00
b = 135.241β = 90.00
c = 142.043γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland147005

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 2.0: 2017-09-06
    Type: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations
  • Version 2.1: 2019-03-20
    Type: Data collection, Derived calculations, Structure summary