5DIR image
Deposition Date 2015-09-01
Release Date 2016-03-02
Last Version Date 2024-10-09
Entry Detail
PDB ID:
5DIR
Keywords:
Title:
membrane protein at 2.8 Angstroms
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Lipoprotein signal peptidase
Gene (Uniprot):lspA
Chain IDs:A, B, C, D
Chain Length:188
Number of Molecules:4
Biological Source:Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Polymer Type:polypeptide(L)
Molecule:Globomycin
Chain IDs:E, F, G, H
Chain Length:5
Number of Molecules:4
Biological Source:synthetic construct
Ligand Molecules
Peptide-like Molecules
PRD_002257
Primary Citation
Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin.
Science 351 876 880 (2016)
PMID: 26912896 DOI: 10.1126/science.aad3747

Abstact

With functions that range from cell envelope structure to signal transduction and transport, lipoproteins constitute 2 to 3% of bacterial genomes and play critical roles in bacterial physiology, pathogenicity, and antibiotic resistance. Lipoproteins are synthesized with a signal peptide securing them to the cytoplasmic membrane with the lipoprotein domain in the periplasm or outside the cell. Posttranslational processing requires a signal peptidase II (LspA) that removes the signal peptide. Here, we report the crystal structure of LspA from Pseudomonas aeruginosa complexed with the antimicrobial globomycin at 2.8 angstrom resolution. Mutagenesis studies identify LspA as an aspartyl peptidase. In an example of molecular mimicry, globomycin appears to inhibit by acting as a noncleavable peptide that sterically blocks the active site. This structure should inform rational antibiotic drug discovery.

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Primary Citation of related structures