1B12

CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor.

Paetzel, M.Dalbey, R.E.Strynadka, N.C.

(1998) Nature 396: 186-190

  • DOI: 10.1038/24196

  • PubMed Abstract: 
  • The signal peptidase (SPase) from Escherichia coli is a membrane-bound endopeptidase with two amino-terminal transmembrane segments and a carboxy-terminal catalytic region which resides in the periplasmic space. SPase functions to release proteins th ...

    The signal peptidase (SPase) from Escherichia coli is a membrane-bound endopeptidase with two amino-terminal transmembrane segments and a carboxy-terminal catalytic region which resides in the periplasmic space. SPase functions to release proteins that have been translocated into the inner membrane from the cell interior, by cleaving off their signal peptides. We report here the X-ray crystal structure of a catalytically active soluble fragment of E. coli SPase (SPase delta2-75). We have determined this structure at 1.9 A resolution in a complex with an inhibitor, a beta-lactam (5S,6S penem), which is covalently bound as an acyl-enzyme intermediate to the gamma-oxygen of a serine residue at position 90, demonstrating that this residue acts as the nucleophile in the hydrolytic mechanism of signal-peptide cleavage. The structure is consistent with the use by SPase of Lys 145 as a general base in the activation of the nucleophilic Ser90, explains the specificity requirement at the signal-peptide cleavage site, and reveals a large exposed hydrophobic surface which could be a site for an intimate association with the membrane. As enzymes that are essential for cell viability, bacterial SPases present a feasible antibacterial target: our determination of the SPase structure therefore provides a template for the rational design of antibiotic compounds.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIGNAL PEPTIDASE I
A, B, C, D
248Escherichia coli (strain K12)Gene Names: lepB
EC: 3.4.21.89
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Peptidases
Protein: 
LepB Signal Peptidase (SPase) in complex with a β-lactam inhibitor
Find proteins for P00803 (Escherichia coli (strain K12))
Go to UniProtKB:  P00803
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
1PN
Query on 1PN

Download SDF File 
Download CCD File 
A, B, C, D
prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate
"(5S,6S)-6-[(R)ACETOXYETH-2-YL]-PENEM-3-CARBOXYLATEPROPANE, Bound form"
C13 H17 N O5 S
KYVQFVHQVGHNFK-UISBYWKRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.700α = 90.00
b = 113.200β = 90.00
c = 99.200γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
CNSrefinement
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-10
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2012-05-09
    Type: Other