4PL0

Crystal structure of the antibacterial peptide ABC transporter McjD in an outward occluded state

Summary for 4PL0

• Entry DOI: 10.2210/pdb4pl0/pdb
• Descriptor: Microcin-J25 export ATP-binding/permease protein McjD, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: abc transporter, membrane protein, occluded, transport protein
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 132638.63

Authors

Choudhury, H.G.,Beis, K. (deposition date: 2014-05-15, release date: 2014-06-18, Last modification date: 2023-12-20)

Primary citation

Choudhury, H.G.,Tong, Z.,Mathavan, I.,Li, Y.,Iwata, S.,Zirah, S.,Rebuffat, S.,van Veen, H.W.,Beis, K.
Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state.
Proc.Natl.Acad.Sci.USA, 111:9145-, 2014

PubMed Abstract: Enterobacteriaceae produce antimicrobial peptides for survival under nutrient starvation. Microcin J25 (MccJ25) is an antimicrobial peptide with a unique lasso topology. It is secreted by the ATP-binding cassette (ABC) exporter McjD, which ensures self-immunity of the producing strain through efficient export of the toxic mature peptide from the cell. Here we have determined the crystal structure of McjD from Escherichia coli at 2.7-Å resolution, which is to the authors' knowledge the first structure of an antibacterial peptide ABC transporter. Our functional and biochemical analyses demonstrate McjD-dependent immunity to MccJ25 through efflux of the peptide. McjD can directly bind MccJ25 and displays a basal ATPase activity that is stimulated by MccJ25 in both detergent solution and proteoliposomes. McjD adopts a new conformation, termed nucleotide-bound outward occluded. The new conformation defines a clear cavity; mutagenesis and ligand binding studies of the cavity have identified Phe86, Asn134, and Asn302 as important for recognition of MccJ25. Comparisons with the inward-open MsbA and outward-open Sav1866 structures show that McjD has structural similarities with both states without the intertwining of transmembrane (TM) helices. The occluded state is formed by rotation of TMs 1 and 2 toward the equivalent TMs of the opposite monomer, unlike Sav1866 where they intertwine with TMs 3-6 of the opposite monomer. Cysteine cross-linking studies on the McjD dimer in inside-out membrane vesicles of E. coli confirmed the presence of the occluded state. We therefore propose that the outward-occluded state represents a transition intermediate between the outward-open and inward-open conformation of ABC exporters.

PubMed: 24920594
DOI: 10.1073/pnas.1320506111

Experimental method

X-RAY DIFFRACTION (2.7 Å)