8VGC image
Deposition Date 2023-12-27
Release Date 2024-02-14
Last Version Date 2024-03-13
Entry Detail
PDB ID:
8VGC
Title:
Complex of ExbD with D-box peptide: Orthorhombic form
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
Resolution:
1.42 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Biopolymer transport protein ExbD
Chain IDs:A, B
Chain Length:83
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GLN-PRO-ILE-SER-VAL-THR-MET-VAL-THR-PRO
Gene (Uniprot):tonB
Chain IDs:C (auth: P)
Chain Length:10
Number of Molecules:1
Biological Source:Escherichia coli
Primary Citation
Discovery and structural characterization of the D-box, a conserved TonB motif that couples an inner-membrane motor to outer-membrane transport.
J.Biol.Chem. 300 105723 105723 (2024)
PMID: 38311172 DOI: 10.1016/j.jbc.2024.105723

Abstact

Gram-negative bacteria use TonB-dependent transport to take up nutrients from the external environment, employing the Ton complex to import a variety of nutrients that are either scarce or too large to cross the outer membrane unaided. The Ton complex contains an inner-membrane motor (ExbBD) that generates force, as well as nutrient-specific transport proteins on the outer membrane. These two components are coupled by TonB, which transmits the force from the inner to the outer membrane. TonB contains an N-terminus anchored in the inner membrane, a C-terminal domain that binds the outer-membrane transporter, and a proline-rich linker connecting the two. While much is known about the interaction between TonB and outer-membrane transporters, the critical interface between TonB and ExbBD is less well understood. Here, we identify a conserved motif within TonB that we term the D-box, which serves as an attachment point for ExbD. We characterize the interaction between ExbD and the D-box both functionally and structurally, showing that a homodimer of ExbD captures one copy of the D-box peptide via beta-strand recruitment. We additionally show that both the D-box motif and ExbD are conserved in a range of Gram-negative bacteria, including members of the ESKAPE group of pathogens. The ExbD:D-box interaction is likely to represent an important aspect of force transduction between the inner and outer membranes. Given that TonB-dependent transport is an important contributor to virulence, this interaction is an intriguing potential target for novel antibacterial therapies.

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Primary Citation of related structures
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