8JF2 image
Deposition Date 2023-05-17
Release Date 2024-05-22
Last Version Date 2025-03-12
Entry Detail
PDB ID:
8JF2
Title:
Cryo-EM structure of tetrameric DltB/DltC complex
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Teichoic acid D-alanyltransferase
Gene (Uniprot):dltB
Chain IDs:A, B, C, D
Chain Length:440
Number of Molecules:4
Biological Source:Streptococcus thermophilus LMG 18311
Polymer Type:polypeptide(L)
Molecule:D-alanyl carrier protein
Gene (Uniprot):dltC
Chain IDs:E (auth: F), F (auth: G), G (auth: H), H (auth: I)
Chain Length:79
Number of Molecules:4
Biological Source:Streptococcus thermophilus LMG 18311
Primary Citation
Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation.
Nat Commun 15 3404 3404 (2024)
PMID: 38649359 DOI: 10.1038/s41467-024-47783-7

Abstact

DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of gram-positive bacteria. This process stabilizes the cell wall structure, influences bacterial virulence, and modulates the host immune response. Despite its significance, the role of DltB is not well understood. Through biochemical analysis and cryo-EM imaging, we discover that Streptococcus thermophilus DltB forms a homo-tetramer on the cell membrane. We further visualize DltB in an apo form, in complex with DltC, and in complex with its inhibitor amsacrine (m-AMSA). Each tetramer features a central hole. The C-tunnel of each protomer faces the intratetramer interface and provides access to the periphery membrane. Each protomer binds a DltC without changing the tetrameric organization. A phosphatidylglycerol (PG) molecule in the substrate-binding site may serve as an LTA carrier. The inhibitor m-AMSA bound to the L-tunnel of each protomer blocks the active site. The tetrameric organization of DltB provides a scaffold for catalyzing D-alanyl transfer and regulating the channel opening and closing. Our findings unveil DltB's dual function in the D-alanylation pathway, and provide insight for targeting DltB as a anti-virulence antibiotic.

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