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 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIGNAL PEPTIDASE I
A, B
250Escherichia coli (strain K12)Mutation(s): 0 
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ARYLOMYCIN A2
C, D
6N/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
M12
Query on M12

Download SDF File 
Download CCD File 
C, D
10-METHYLUNDECANOIC ACID
C12 H24 O2
QJRRBVNPIKYRQJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000117
Query on PRD_000117
C,DARYLOMYCIN A2Lipopeptide / Antibiotic

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ARYKd: 940 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.609α = 90.00
b = 69.609β = 90.00
c = 258.466γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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