Crystal structure of the bacterial antitoxin HigA from Escherichia coli at pH 8.5. Northeast Structural Genomics TARGET ER390.

Experimental Data Snapshot

  • Resolution: 1.63 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.198 

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Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems.

Arbing, M.A.Handelman, S.K.Kuzin, A.P.Verdon, G.Wang, C.Su, M.Rothenbacher, F.P.Abashidze, M.Liu, M.Hurley, J.M.Xiao, R.Acton, T.Inouye, M.Montelione, G.T.Woychik, N.A.Hunt, J.F.

(2010) Structure 18: 996-1010

  • DOI: https://doi.org/10.1016/j.str.2010.04.018
  • Primary Citation of Related Structures:  
    2H28, 2ICT, 2INW, 3KH2

  • PubMed Abstract: 

    Bacterial toxin-antitoxin (TA) systems serve a variety of physiological functions including regulation of cell growth and maintenance of foreign genetic elements. Sequence analyses suggest that TA families are linked by complex evolutionary relationships reflecting likely swapping of functional domains between different TA families. Our crystal structures of Phd-Doc from bacteriophage P1, the HigA antitoxin from Escherichia coli CFT073, and YeeU of the YeeUWV systems from E. coli K12 and Shigella flexneri confirm this inference and reveal additional, unanticipated structural relationships. The growth-regulating Doc toxin exhibits structural similarity to secreted virulence factors that are toxic for eukaryotic target cells. The Phd antitoxin possesses the same fold as both the YefM and NE2111 antitoxins that inhibit structurally unrelated toxins. YeeU, which has an antitoxin-like activity that represses toxin expression, is structurally similar to the ribosome-interacting toxins YoeB and RelE. These observations suggest extensive functional exchanges have occurred between TA systems during bacterial evolution.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, 702 Fairchild Center, MC2434, New York, NY 10027, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
antitoxin higa94Escherichia coli CFT073Mutation(s): 0 
Gene Names: higa
Find proteins for P67700 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P67700 
Go to UniProtKB:  P67700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67700
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.63 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.535α = 90
b = 26.364β = 91.51
c = 39.485γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description