4X8B

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 ?
R-Value Free: 0.157
R-Value Work: 0.138
R-Value Observed: 0.139

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

PubMed: 25597398 Search on PubMed
DOI: https://doi.org/10.1002/anie.201410045
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G7CFI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain S [auth B]	J [auth A], S [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain S [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B]	K [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B]	H [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain Q [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B]	I [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 ?
R-Value Free: 0.157
R-Value Work: 0.138
R-Value Observed: 0.139
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( ? )	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

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Entry History & Funding Information

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	1147005

Revision History (Full details and data files)

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

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Help and Resources

4X8B

Ergothioneine-biosynthetic sulfoxide synthase EgtB, apo form

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)