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 1.1 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 / PAO1 / 1C / PRS 101 / LMG 12228)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 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  Q9HVM5
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A, B, C, D
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
MLE
Query on MLE

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Download CCD File 
A, B, C, D
N-METHYLLEUCINE
C7 H15 N O2
XJODGRWDFZVTKW-LURJTMIESA-N
 Ligand Interaction
IIL
Query on IIL

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Download CCD File 
A, B, C, D
ISO-ISOLEUCINE
ALLO-ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-UHNVWZDZSA-N
 Ligand Interaction
5BV
Query on 5BV

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Download CCD File 
A, B, C, D
(2R,3R)-3-(glycyloxy)-2-methylnonanoic acid
C12 H23 N O4
UBRONVWKPIWEHT-NXEZZACHSA-N
 Ligand Interaction
SER
Query on SER

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Download CCD File 
A, B, C, D
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
ALO
Query on ALO

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Download CCD File 
A, B, C, D
ALLO-THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-HRFVKAFMSA-N
 Ligand Interaction
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
PHENIXphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant 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