4X8B | pdb_00004x8b

Ergothioneine-biosynthetic sulfoxide synthase EgtB, apo form

• PDB DOI: https://doi.org/10.2210/pdb4X8B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-10 Released: 2015-01-28 
• Deposition Author(s): Vit, A., Goncharenko, K.V., Blankenfeldt, W., Seebeck, F.P.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.157 (Depositor), 0.141 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

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

• PubMed: 25597398 
• DOI: https://doi.org/10.1002/anie.201410045
• Primary Citation Related Structures: 
  4X8B, 4X8D, 4X8E


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 100.36 kDa 
• Atom Count: 8,053 
• Modeled Residue Count: 854 
• Deposited Residue Count: 894 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfoxide synthase EgtB	A, B	447	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0  Gene Names: KEK_08772 EC: 1.14.99.50
UniProt
Find proteins for G7CFI3 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CFI3  Go to UniProtKB:  G7CFI3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	J [auth A], S [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	K [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.157 (Depositor), 0.141 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.78	α = 90
b = 134.78	β = 90
c = 141.204	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
SHELXDE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
ARP	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Vit, A., Goncharenko, K.V., Blankenfeldt, W., Seebeck, F.P.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	1147005

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 2.0: 2017-09-06
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary