6N90

YoeB/ParE toxin from Agrobacterium tumefaciens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

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This is version 1.3 of the entry. See complete history


Literature

Identifying a Molecular Mechanism That Imparts Species-Specific Toxicity to YoeB Toxins.

Ames, J.R.McGillick, J.Murphy, T.Reddem, E.Bourne, C.R.

(2020) Front Microbiol 11: 959-959

  • DOI: https://doi.org/10.3389/fmicb.2020.00959
  • Primary Citation of Related Structures:  
    6N90

  • PubMed Abstract: 

    The ribosome-dependent E. coli (Ec) mRNase toxin YoeB has been demonstrated to protect cells during thermal stress. Agrobacterium tumefaciens (At), a plant pathogen, also encodes a YoeB toxin. Initial studies indicated that AtYoeB does not impact the growth of Ec, but its expression is toxic to the native host At. The current work examines this species-specific effect. We establish the highly similar structure and function of Ec and AtYoeB toxins, including the ability of the AtYoeB toxin to inhibit Ec ribosomes in vitro . Comparison of YoeB sequences and structures highlights a four-residue helix between β-strands 2 and 3 that interacts with mRNA bases within the ribosome. This helix sequence is varied among YoeB toxins, and this variation correlates with bacterial classes of proteobacteria. When the four amino acid sequence of this helix is transplanted from EcYoeB onto AtYoeB, the resulting chimera gains toxicity to Ec cells and lessens toxicity to At cells. The reverse is also true, such that EcYoeB with the AtYoeB helix sequence is less toxic to Ec and gains toxicity to At cultures. We suggest this helix sequence directs mRNA sequence-specific degradation, which varies among proteobacterial classes, and thus controls growth inhibition and YoeB toxicity.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
95Agrobacterium tumefaciensMutation(s): 0 
Gene Names: Atu2017
UniProt
Find proteins for A9CID9 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CID9 
Go to UniProtKB:  A9CID9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CID9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TEW
Query on TEW

Download Ideal Coordinates CCD File 
C [auth B]6-tungstotellurate(VI)
O24 Te W6
JDLYBIMRCSJRQJ-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.955α = 90
b = 77.739β = 92.91
c = 36.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM103640

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-07-22
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description