5DIR

membrane protein at 2.8 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin.

Vogeley, L.El Arnaout, T.Bailey, J.Stansfeld, P.J.Boland, C.Caffrey, M.

(2016) Science 351: 876-880

  • DOI: 10.1126/science.aad3747

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein signal peptidase
A, B, C, D
188Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: lspA (ls)
EC: 3.4.23.36
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Intramembrane Proteases
Protein: 
Lipoprotein signal peptidase II
Find proteins for Q9HVM5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HVM5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Globomycin
E, F, G, H
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A, B, C, D, F
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
MLE
Query on MLE
E, F, G, H
L-PEPTIDE LINKINGC7 H15 N O2LEU
IIL
Query on IIL
E, F, G, H
L-PEPTIDE LINKINGC6 H13 N O2ILE
5BV
Query on 5BV
E, F, G, H
NON-POLYMERC12 H23 N O4

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ALO
Query on ALO
E, F, G, H
L-PEPTIDE LINKINGC4 H9 N O3THR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.480α = 90.00
b = 105.880β = 96.92
c = 85.390γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 2.0: 2019-06-19
    Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary