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 

Starting Model: experimental
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This is version 2.0 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: https://doi.org/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 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIGNAL PEPTIDASE I
A, B
250Escherichia coliMutation(s): 0 
Gene Names: LEPB
EC: 3.4.21.89
Membrane Entity: Yes 
UniProt
Find proteins for P00803 (Escherichia coli (strain K12))
Explore P00803 
Go to UniProtKB:  P00803
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00803
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ARYLOMYCIN A2
C, D
6Streptomyces sp.Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
5PG
Query on 5PG
C, D
L-PEPTIDE LINKINGC9 H11 N O3GLY
Biologically Interesting Molecules (External Reference) 1 Unique
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description