4HZ9

Crystal structure of the type VI native effector-immunity complex Tae3-Tai3 from Ralstonia pickettii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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This is version 1.1 of the entry. See complete history. 


Literature

Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3

Dong, C., Zhang, H., Gao, Z.Q., Wang, W.J., She, Z., Liu, G.F., Shen, Y.Q., Su, X.D., Dong, Y.H.

(2013) Biochem J 454: 59-68

  • DOI: 10.1042/BJ20130193
  • Primary Citation of Related Structures:  
    4HZ9, 4HZB

  • PubMed Abstract: 

    • The recently described T6SS (type VI secretion system) acts as a needle that punctures the membrane of the target cells to deliver effector proteins. Type VI amidase effectors can be classified into four divergent families (Tae1-Tae4). These effectors are secreted into the periplasmic space of neighbouring cells via the T6SS and subsequently rupture peptidoglycan ...

    The recently described T6SS (type VI secretion system) acts as a needle that punctures the membrane of the target cells to deliver effector proteins. Type VI amidase effectors can be classified into four divergent families (Tae1-Tae4). These effectors are secreted into the periplasmic space of neighbouring cells via the T6SS and subsequently rupture peptidoglycan. However, the donor cells are protected from damage because of the presence of their cognate immunity proteins [Tai1 (type VI amidase immunity 1)-Tai4]. In the present paper, we describe the structure of Tae3 in complex with Tai3. The Tae3-Tai3 complex exists as a stable heterohexamer, which is composed of two Tae3 molecules and two Tai3 homodimers (Tae3-Tai34-Tae3). Tae3 shares a common NlpC/P60 fold, which consists of N-terminal and C-terminal subdomains. Structural analysis indicates that two unique loops around the catalytic cleft adopt a closed conformation, resulting in a narrow and extended groove involved in the binding of the substrate. The inhibition of Tae3 is attributed to the insertion of the Ω-loop (loop of α3-α4) of Tai3 into the catalytic groove. Furthermore, a cell viability assay confirmed that a conserved motif (Gln-Asp-Xaa) in Tai3 members may play a key role in the inhibition process. Taken together, the present study has revealed a novel inhibition mechanism and provides insights into the role played by T6SS in interspecific competition.

    Organizational Affiliation: 

    State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative cytoplasmic proteinA119Ralstonia pickettii 12DMutation(s): 0 
Gene Names: Rpic12D_3260
UniProt
Find proteins for C6BHF2 (Ralstonia pickettii (strain 12D))
Explore C6BHF2 
Go to UniProtKB:  C6BHF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6BHF2
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative periplasmic proteinB, C150Ralstonia pickettii 12DMutation(s): 0 
Gene Names: Rpic12D_3261
UniProt
Find proteins for C6BHF3 (Ralstonia pickettii (strain 12D))
Explore C6BHF3 
Go to UniProtKB:  C6BHF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6BHF3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.166α = 90
b = 144.382β = 90
c = 129.908γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
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: 2013-08-21
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description