3SLT

Pre-cleavage Structure of the Autotransporter EspP - N1023S Mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

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This is version 1.3 of the entry. See complete history. 


Literature

Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter.

Barnard, T.J., Gumbart, J., Peterson, J.H., Noinaj, N., Easley, N.C., Dautin, N., Kuszak, A.J., Tajkhorshid, E., Bernstein, H.D., Buchanan, S.K.

(2012) J Mol Biol 415: 128-142

  • DOI: 10.1016/j.jmb.2011.10.049
  • Primary Citation of Related Structures:  
    3SLJ, 3SLO, 3SLT

  • PubMed Abstract: 

    • Autotransporters are secreted proteins produced by pathogenic Gram-negative bacteria. They consist of a membrane-embedded β-domain and an extracellular passenger domain that is sometimes cleaved and released from the cell surface. We solved the structures of three noncleavable mutants of the autotransporter EspP to examine how it promotes asparagine cyclization to cleave its passenger ...

    Autotransporters are secreted proteins produced by pathogenic Gram-negative bacteria. They consist of a membrane-embedded β-domain and an extracellular passenger domain that is sometimes cleaved and released from the cell surface. We solved the structures of three noncleavable mutants of the autotransporter EspP to examine how it promotes asparagine cyclization to cleave its passenger. We found that cyclization is facilitated by multiple factors. The active-site asparagine is sterically constrained to conformations favorable for cyclization, while electrostatic interactions correctly orient the carboxamide group for nucleophilic attack. During molecular dynamics simulations, water molecules were observed to enter the active site and to form hydrogen bonds favorable for increasing the nucleophilicity of the active-site asparagine. When the activated asparagine attacks its main-chain carbonyl carbon, the resulting oxyanion is stabilized by a protonated glutamate. Upon cleavage, this proton could be transferred to the leaving amine group, helping overcome a significant energy barrier. Together, these findings provide insight into factors important for asparagine cyclization, a mechanism broadly used for protein cleavage.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease espPA313Escherichia coli O157:H7Mutation(s): 1 
Gene Names: ECO57PM78, espP, L7020
EC: 3.4.21
Membrane Entity: Yes 
UniProt
Find proteins for Q7BSW5 (Escherichia coli O157:H7)
Explore Q7BSW5 
Go to UniProtKB:  Q7BSW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7BSW5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.162α = 90
b = 122.372β = 90
c = 122.098γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-11-30
    Changes: Database references
  • Version 1.2: 2012-01-18
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description