28OJ
X-ray crystal structure of wild-type YdbL from Escherichia coli
Summary for 28OJ
| Entry DOI | 10.2210/pdb28oj/pdb |
| Descriptor | Probable chaperone-like protein YdbL (2 entities in total) |
| Functional Keywords | bacterial, globular, periplasmic, unknown function |
| Biological source | Escherichia coli BW25113 |
| Total number of polymer chains | 1 |
| Total formula weight | 9728.00 |
| Authors | |
| Primary citation | De'Ath, C.,Kumar, S.,Chhibber, S.,Cooper, B.F.,Taylor, E.,Jones, E.,Lanyon-Hogg, T.,Bolla, J.,Redfield, C.,Ruiz, N.,Isom, G. YdbL directly modulates YdbH-YnbE bridge formation to maintain Escherichia coli outer membrane homeostasis. Biorxiv, 2026 Cited by PubMed Abstract: Gram-negative bacteria pose a threat to global healthcare mainly because their outer membrane (OM) provides an intrinsic barrier to many antimicrobials. Key to this barrier function is the asymmetric structure of the OM, with phospholipids constituting the inner leaflet and lipopolysaccharides the outer leaflet. Although the mechanism of phospholipid transport between the inner membrane (IM) and OM remains poorly understood, recent studies implicate TamB, YhdP, and YdbH as functionally redundant proteins mediating this process in Escherichia coli. Accordingly, collective loss of these three paralogs is lethal and any one of them is sufficient for growth. YdbH is anchored to the IM and its periplasmic repeating β-sheet groove domain interacts with the OM lipoprotein YnbE via β-strand augmentation to form an intermembrane bridge. Additionally, YnbE multimerizes, and the periplasmic protein YdbL is proposed to modulate YnbE multimerization to facilitate its stacking on the C-terminus of YdbH. Here, we demonstrate that excess YdbL specifically inhibits the function of the YdbH-YnbE complex since overexpression of ydbL causes lethality in the ΔyhdP ΔtamB double mutant but the presence of both ydbH and ynbE in trans abrogates this lethality. We resolve high-resolution structural data for YdbL and ascertain its interaction site with the YnbE C-terminal 𝛼-helix, with residues mediating this interface highly conserved and critical for YdbL function. Finally, we show that YdbL is protected from degradation by the protease DegP when complexed with YnbE. Overall, our data supports a model in which YdbL ensures proper YdbH-YnbE intermembrane bridge formation by directly interacting with YnbE. PubMed: 41889818DOI: 10.64898/2026.03.16.712125 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.12 Å) |
Structure validation
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