1T7D

Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystallographic and Biophysical Analysis of a Bacterial Signal Peptidase in Complex with a Lipopeptide Based Inhibitor.

Paetzel, M.Goodall, J.J.Kania, M.Dalbey, R.E.Page, M.G.P.

(2004) J Biol Chem 279: 30781

  • DOI: 10.1074/jbc.M401686200
  • Primary Citation of Related Structures:  
    1T7D

  • PubMed Abstract: 
  • We report here the crystallographic and biophysical analysis of a soluble, catalytically active fragment of the Escherichia coli type I signal peptidase (SPase Delta2-75) in complex with arylomycin A2. The 2.5-A resolution structure revealed that the ...

    We report here the crystallographic and biophysical analysis of a soluble, catalytically active fragment of the Escherichia coli type I signal peptidase (SPase Delta2-75) in complex with arylomycin A2. The 2.5-A resolution structure revealed that the inhibitor is positioned with its COOH-terminal carboxylate oxygen (O45) within hydrogen bonding distance of all the functional groups in the catalytic center of the enzyme (Ser90 O-gamma, Lys145 N-zeta, and Ser88 O-gamma) and that it makes beta-sheet type interactions with the beta-strands that line each side of the binding site. Ligand binding studies, calorimetry, fluorescence spectroscopy, and stopped-flow kinetics were also used to analyze the binding mode of this unique non-covalently bound inhibitor. The crystal structure was solved in the space group P4(3)2(1)2. A detailed comparison is made to the previously published acyl-enzyme inhibitor complex structure (space group: P2(1)2(1)2) and the apo-enzyme structure (space group: P4(1)2(1)2). Together this work provides insights into the binding of pre-protein substrates to signal peptidase and will prove helpful in the development of novel antibiotics.


    Related Citations: 
    • Crystal Structure of a Bacterial Signal Peptidase Apoenzyme: Implications for Signal Peptide Binding and the Ser-Lys Dyad Mechanism
      Paetzel, M., Dalbey, R.E., Strynadka, N.C.
      (2002) J Biol Chem 277: 9512
    • 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

    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada. mpaetze@sfu.ca



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIGNAL PEPTIDASE IAB250Escherichia coliMutation(s): 0 
Gene Names: lepB
EC: 3.4.21.89
Membrane protein
Mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Peptidases
Protein: 
LepB Signal Peptidase (SPase) in complex with a lipopeptide inhibitor
Find proteins for P00803 (Escherichia coli (strain K12))
Explore P00803 
Go to UniProtKB:  P00803
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ARYLOMYCIN A2CD6Streptomyces sp.Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M12
Query on M12

Download CCD File 
C, D
10-METHYLUNDECANOIC ACID
C12 H24 O2
QJRRBVNPIKYRQJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5PG
Query on 5PG
C,DL-PEPTIDE LINKINGC9 H11 N O3GLY
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ARYKd :  940   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000117
Query on PRD_000117
C, DARYLOMYCIN A2Lipopeptide /  Antibiotic

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.609α = 90
b = 69.609β = 90
c = 258.466γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other