6SM3

Structure of the RagAB peptide importer in the 'closed-closed' state

Summary for 6SM3

• Entry DOI: 10.2210/pdb6sm3/pdb
• Related: 6SLI 6SLJ 6SLN
• EMDB information: 10241
• Descriptor: Lipoprotein RagB, RagA protein, GLY-GLY-ALA-THR-THR-ALA-THR-THR-THR-THR-SER-THR-SER, ... (5 entities in total)
• Functional Keywords: beta-barrel, omp, tonb-dependent, transporter, membrane protein
• Biological source: Porphyromonas gingivalis (strain ATCC BAA-308 / W83); More
• Total number of polymer chains: 3
• Total formula weight: 157428.14

Authors

White, J.B.R.,Ranson, N.A.,van den Berg, B. (deposition date: 2019-08-21, release date: 2020-05-20, Last modification date: 2025-04-09)

Primary citation

Madej, M.,White, J.B.R.,Nowakowska, Z.,Rawson, S.,Scavenius, C.,Enghild, J.J.,Bereta, G.P.,Pothula, K.,Kleinekathoefer, U.,Basle, A.,Ranson, N.A.,Potempa, J.,van den Berg, B.
Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.
Nat Microbiol, 5:1016-1025, 2020

PubMed Abstract: Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagAB complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis.

PubMed: 32393857
DOI: 10.1038/s41564-020-0716-y

Experimental method

ELECTRON MICROSCOPY (3.3 Å)