7PPZ

Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in complex with human eIF4A - Crystal form A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of specificity and deamidation of eIF4A by Burkholderia Lethal Factor 1.

Mobbs, G.W.Aziz, A.A.Dix, S.R.Blackburn, G.M.Sedelnikova, S.E.Minshull, T.C.Dickman, M.J.Baker, P.J.Nathan, S.Raih, M.F.Rice, D.W.

(2022) Commun Biol 5: 272-272

  • DOI: https://doi.org/10.1038/s42003-022-03186-2
  • Primary Citation of Related Structures:  
    6RVU, 7PPZ, 7PQ0

  • PubMed Abstract: 

    Burkholderia pseudomallei lethal factor 1 (BLF1) exhibits site-specific glutamine deamidase activity against the eukaryotic RNA helicase, eIF4A, thereby blocking mammalian protein synthesis. The structure of a complex between BLF1 C94S and human eIF4A shows that the toxin binds in the cleft between the two RecA-like eIF4A domains forming interactions with residues from both and with the scissile amide of the target glutamine, Gln339, adjacent to the toxin active site. The RecA-like domains adopt a radically twisted orientation compared to other eIF4A structures and the nature and position of conserved residues suggests this may represent a conformation associated with RNA binding. Comparison of the catalytic site of BLF1 with other deamidases and cysteine proteases reveals that they fall into two classes, related by pseudosymmetry, that present either the re or si faces of the target amide/peptide to the nucleophilic sulfur, highlighting constraints in the convergent evolution of their Cys-His active sites.


  • Organizational Affiliation

    Krebs Institute, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Burkholderia Lethal Factor 1 (BLF1)211Burkholderia pseudomallei K96243Mutation(s): 1 
Gene Names: BPSL1549
UniProt
Find proteins for Q63UP7 (Burkholderia pseudomallei (strain K96243))
Explore Q63UP7 
Go to UniProtKB:  Q63UP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63UP7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-I394Homo sapiensMutation(s): 0 
Gene Names: EIF4A1DDX2AEIF4A
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P60842 (Homo sapiens)
Explore P60842 
Go to UniProtKB:  P60842
PHAROS:  P60842
GTEx:  ENSG00000161960 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60842
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.98α = 90
b = 50.36β = 111.92
c = 95.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited KingdomIC170306
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M012166/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description