7Z6F | pdb_00007z6f

Crystal structure of the substrate-binding protein YejA in complex with peptide fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Z6F

This is version 1.2 of the entry. See complete history

Literature

Trojan horse peptide conjugates remodel the activity spectrum of clinical antibiotics.

Luo, S.Li, X.R.Gong, X.T.Kulikovsky, A.Qu, F.Beis, K.Severinov, K.Dubiley, S.Feng, X.Dong, S.H.Nair, S.K.

(2025) Proc Natl Acad Sci U S A 122: e2319483121-e2319483121

  • DOI: https://doi.org/10.1073/pnas.2319483121
  • Primary Citation Related Structures: 
    7Z6F, 8FSQ, 8FSR, 8FSS

  • PubMed Abstract: 

    Infections caused by gram-negative pathogens continue to be a major risk to human health because of the innate antibiotic resistance endowed by their unique cell membrane architecture. Nature has developed an elegant solution to target gram-negative strains, namely by conjugating toxic antibiotic warheads to a suitable carrier to facilitate the active import of the drug to a specific target organism. Microcin C7 (McC) is a Trojan horse peptide-conjugated antibiotic that specifically targets enterobacteria by exploiting active import through oligopeptide transport systems. Here, we characterize the molecular mechanism of McC recognition by YejA, the solute binding protein of the Escherichia coli oligopeptide transporter. Structure-guided mutational and functional analysis elucidates the determinants of substrate recognition. We demonstrate that the peptide carrier can serve as a passport for the entry of molecules that are otherwise not taken into E. coli cells. We show that peptide conjugation can remodel the antibiotic spectrum of clinically relevant parent compounds. Bioinformatics analysis reveals a broad distribution of YejA-like transporters in only the Proteobacteria, underscoring the potential for the development of Trojan horse antibiotics that are actively imported into such gram-negative bacteria.


  • Organizational Affiliation
    • State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 69.45 kDa 
  • Atom Count: 5,471 
  • Modeled Residue Count: 593 
  • Deposited Residue Count: 597 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YejAA [auth E]585Escherichia coliMutation(s): 0 
Gene Names: yejAb2177JW2165
UniProt
Find proteins for P33913 (Escherichia coli (strain K12))
Explore P33913 
Go to UniProtKB:  P33913
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33913
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
degradation peptide VAL-LEU-GLY-GLU-PRO-ARG-TYR-ALA-PHE-ASN-PHE-ASNB [auth A]12Escherichia coliMutation(s): 0 
UniProt
Find proteins for P33913 (Escherichia coli (strain K12))
Explore P33913 
Go to UniProtKB:  P33913
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33913
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.531α = 90
b = 76.972β = 90
c = 103.817γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N020103/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Database references, Structure summary
  • Version 1.2: 2026-03-04
    Changes: Refinement description