7OT9 | pdb_00007ot9

Structure of the AI-2 exporter family protein YdiK from E. coli

• PDB DOI: https://doi.org/10.2210/pdb7OT9/pdb
• EM Map EMD-13057: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-06-09 Released: 2022-05-11 
• Deposition Author(s): Khera, R., Xie, H., Michel, H.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism.

Khera, R., Mehdipour, A.R., Bolla, J.R., Kahnt, J., Welsch, S., Ermler, U., Muenke, C., Robinson, C.V., Hummer, G., Xie, H., Michel, H.

(2022) EMBO J 41: e109990-e109990

• PubMed: 35698912 
• DOI: https://doi.org/10.15252/embj.2021109990
• Primary Citation Related Structures: 
  7NB6, 7OT9


• PubMed Abstract: 
  

  Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis, and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from Escherichia coli, which belongs to the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism.

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Organizational Affiliation: 
• Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Centre for molecular modelling, Ghent University, Zwijnaarde, Belgium.
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
The Kavli Institute for Nanoscience Discovery, Oxford, UK.
Department of Plant Sciences, University of Oxford, Oxford, UK.
Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, mass spectrometry, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 199.33 kDa 
• Atom Count: 8,410 
• Modeled Residue Count: 1,105 
• Deposited Residue Count: 1,850 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AI-2E member YdiK	A, B [auth E], C [auth D], D [auth C], E [auth B]	370	Escherichia coli K-12	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0AFS7 (Escherichia coli (strain K12)) Explore P0AFS7  Go to UniProtKB:  P0AFS7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-11 
Deposition Author(s): Khera, R., Xie, H., Michel, H.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release
  
• Version 1.1: 2022-12-14
  Changes: Database references
• Version 1.2: 2024-07-17
  Changes: Data collection