6QKJ

EgtB from Chloracidobacterium thermophilum, a type II sulfoxide synthase in complex with N,N,N-trimethyl-histidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An Alternative Active Site Architecture for O2Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum.

Stampfli, A.R.Goncharenko, K.V.Meury, M.Dubey, B.N.Schirmer, T.Seebeck, F.P.

(2019) J Am Chem Soc 141: 5275-5285

  • DOI: https://doi.org/10.1021/jacs.8b13023
  • Primary Citation of Related Structures:  
    6QKI, 6QKJ

  • PubMed Abstract: 

    Sulfoxide synthases are nonheme iron enzymes that catalyze oxidative carbon-sulfur bond formation between cysteine derivatives and N-α-trimethylhistidine as a key step in the biosynthesis of thiohistidines. The complex catalytic mechanism of this enzyme reaction has emerged as the controversial subject of several biochemical and computational studies. These studies all used the structure of the γ-glutamyl cysteine utilizing sulfoxide synthase, MthEgtB from Mycobacterium thermophilum (EC 1.14.99.50), as a structural basis. To provide an alternative model system, we have solved the crystal structure of CthEgtB from Chloracidobacterium thermophilum (EC 1.14.99.51) that utilizes cysteine as a sulfur donor. This structure reveals a completely different configuration of active site residues that are involved in oxygen binding and activation. Furthermore, comparison of the two EgtB structures enables a classification of all ergothioneine biosynthetic EgtBs into five subtypes, each characterized by unique active-site features. This active site diversity provides an excellent platform to examine the catalytic mechanism of sulfoxide synthases by comparative enzymology, but also raises the question as to why so many different solutions to the same biosynthetic problem have emerged.


  • Organizational Affiliation

    Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
437Chloracidobacterium thermophilum BMutation(s): 0 
Gene Names: Cabther_A1318
UniProt
Find proteins for G2LET6 (Chloracidobacterium thermophilum (strain B))
Explore G2LET6 
Go to UniProtKB:  G2LET6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2LET6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AVJ
Query on AVJ

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
N,N,N-trimethyl-histidine
C9 H16 N3 O2
GPPYTCRVKHULJH-QMMMGPOBSA-O
IMD
Query on IMD

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
G [auth A],
I [auth B],
M [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.143α = 90
b = 201.288β = 90
c = 108.332γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilSwitzerlandERC-2013- StG 336559

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations, Refinement description