9O6A | pdb_00009o6a

CryoEM structure of EcKatG S-Trp105 at 2.22 Angstrom resolution revealing an asymmetric sulfur center in O=S-Trp

• PDB DOI: https://doi.org/10.2210/pdb9O6A/pdb
• EM Map EMD-70168: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-11 Released: 2026-04-22 
• Deposition Author(s): Duan, R., Li, J., Nathan, B., Yang, X., Liu, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Single-atom substitution redirects KatG reactivity from cofactor biogenesis to stereoselective sulfoxidation.

Duan, R., Li, J., Griffith, W.P., Xu, Y., Burrows, N.D., Green, A.P., Liu, A.

(2026) Nat Commun 17

• PubMed: 42288482 
• DOI: https://doi.org/10.1038/s41467-026-73579-y
• Primary Citation Related Structures: 
  9O6A


• PubMed Abstract: 
  

  Protein-derived cofactors rely on precisely positioned heteroatoms to direct redox chemistry, yet isolating their individual contributions remains challenging. The indole N-H of tryptophan plays a central yet elusive role in biogenesis and function of the Met-Tyr-Trp (MYW) cofactor in catalase-peroxidase (KatG). Here, we use genetic code expansion to replace cofactor-forming Trp105 with thiotryptophan (S-Trp), enabling a single-heteroatom (N → S) substitution. Instead of forming the MYW crosslink, KatG bearing S-Trp105 undergoes site-specific monooxygenation to yield a chiral sulfoxide. HPLC-MS, circular dichroism, and FT-IR spectroscopy identify selective oxygen insertion at the sulfur, establishing enantioselective formation of an (S)-configured sulfoxide. A 2.22 Å cryo-EM structure visualizes the oxidized S-Trp105, revealing the S = O moiety orienting toward the iron and confirming the absence of crosslinking. The S-atom oxygenation is heme-dependent and proceeds via a two-electron oxygen-atom transfer, contrasting with the radical-mediated one-electron chemistry of native tryptophan. This redirection suppresses catalase activity by perturbing cofactor formation. These results show that a single-atom substitution reroutes the distal heme site from radical crosslinking to stereoselective sulfoxidation, uncovering a monooxygenase-like capability within KatG. This work highlights using noncanonical amino acids to achieve atomic-level control over reaction pathways and to interrogate cofactor biogenesis with unprecedented precision.

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Organizational Affiliation: 
• Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.
Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, P. R. China.
Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX, 78249, USA. [e-mail].
Department of Biochemistry and Biophysics, and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 326.89 kDa 
• Atom Count: 20,360 
• Modeled Residue Count: 2,576 
• Deposited Residue Count: 2,932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B, C, D	733	Escherichia coli K-12	Mutation(s): 0  Gene Names: katG, ECDH10B_4131 EC: 1.11.1.21
UniProt
Find proteins for B1XBA8 (Escherichia coli (strain K12 / DH10B)) Explore B1XBA8  Go to UniProtKB:  B1XBA8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1B9V	A, B, C, D	L-PEPTIDE LINKING	C11 H13 N O3 S		TRP

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0rc1_5599
RECONSTRUCTION	cryoSPARC	4.5.3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Duan, R., Li, J., Nathan, B., Yang, X., Liu, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM152982

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release
  
• Version 1.1: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.2: 2026-08-19
  Changes: Data collection, Database references