4X8D

Ergothioneine-biosynthetic sulfoxide synthase EgtB in complex with N,N-dimethyl-histidine and gamma-glutamyl-cysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 2.0 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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 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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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3GC
Query on 3GC

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A, B
GAMMA-GLUTAMYLCYSTEINE
C8 H14 N2 O5 S
RITKHVBHSGLULN-WHFBIAKZSA-N
 Ligand Interaction
AVI
Query on AVI

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Download CCD File 
A, B
N,N-dimethyl-L-histidine
C8 H13 N3 O2
IMOBSLOLPCWZKQ-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.292α = 90.00
b = 135.292β = 90.00
c = 141.293γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
PHENIXrefinement
Aimlessdata scaling

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, Derived calculations