9EGI | pdb_00009egi

Crystal Structure of EgtUC binding domain mutant T274G bound to L-Ergothioneine from S. pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb9EGI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae D39
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-11-21 Released: 2025-11-26 
• Deposition Author(s): Legg, K.A., Gonzalez-Gutierrez, G., Giedroc, D.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

CH•••S hydrogen bonds drive molecular recognition of ergothioneine by the microbial transporter.

Legg, K.A., Gonzalez-Gutierrez, G., Edmonds, K.A., Shushkov, P.G., Giedroc, D.P.

(2026) Sci Adv 12: eaeb0426-eaeb0426

• PubMed: 41719410 
• DOI: https://doi.org/10.1126/sciadv.aeb0426
• Primary Citation Related Structures: 
  9EGH, 9EGI, 9EGJ, 9O5F


• PubMed Abstract: 
  

  Many bacteria harbor an ATP-binding cassette (ABC) transporter named EgtU specific for the human dietary antioxidant and 2-thioimidazole-containing low-molecular weight thiol ergothioneine (ET). How the solute binding domain, EgtUC, discriminates among ET and other similar molecules is unknown. Here, we use a "chimeric" mutagenesis strategy and two distantly related EgtUCs from Streptococcus pneumoniae and Helicobacter pylori to show that a suite of EgtUC alkyl CH•••S hydrogen bonds to the ET thione S atom are central determinants of molecular recognition. Small perturbations in CH•••S distance and angle give rise to sharply attenuated transport-competent ET-bound "closed" state lifetimes and increased motional disorder in the binding pocket, not around the S atom itself, but distally in weakening NH•••O hydrogen bonds. This work highlights the impact of alkyl CH•••S H bonding in a biological protein-ligand complex in water.

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Organizational Affiliation: 
• Department of Chemistry, Indiana University, Bloomington, IN, USA.
Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 62.51 kDa 
• Atom Count: 4,591 
• Modeled Residue Count: 547 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ergothioneine transporter EgtUC	A, B	277	Streptococcus pneumoniae D39	Mutation(s): 1  Gene Names: proWX, SPD_1642
UniProt
Find proteins for A0A0H2ZQB9 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZQB9  Go to UniProtKB:  A0A0H2ZQB9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LW8 (Subject of Investigation/LOI)	C [auth A], D [auth B]	trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium C9 H16 N3 O2 S SSISHJJTAXXQAX-ZETCQYMHSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.153	α = 90
b = 127.313	β = 90
c = 206.655	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Legg, K.A., Gonzalez-Gutierrez, G., Giedroc, D.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118157

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2026-04-15
  Changes: Database references