7MU9

Solution NMR structure of the XVIPCD region from the T4SS effector X-Tfe(XAC2609) from Xanthomonas citri


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for effector recognition by an antibacterial type IV secretion system.

Oka, G.U.Souza, D.P.Cenens, W.Matsuyama, B.Y.Cardoso, M.V.C.Oliveira, L.C.da Silva Lima, F.Cuccovia, I.M.Guzzo, C.R.Salinas, R.K.Farah, C.S.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2112529119
  • Primary Citation of Related Structures:  
    7MU9

  • PubMed Abstract: 

    Many soil-, water-, and plant-associated bacterial species from the orders Xanthomonadales, Burkholderales, and Neisseriales carry a type IV secretion system (T4SS) specialized in translocating effector proteins into other gram-negative species, leading to target cell death. These effectors, known as X-Tfes, carry a carboxyl-terminal domain of ∼120 residues, termed XVIPCD, characterized by several conserved motifs and a glutamine-rich tail. Previous studies showed that the XVIPCD is required for interaction with the T4SS coupling protein VirD4 and for T4SS-dependent translocation. However, the structural basis of the XVIPCD-VirD4 interaction is unknown. Here, we show that the XVIPCD interacts with the central all-alpha domain of VirD4 (VirD4 AAD ). We used solution NMR spectroscopy to solve the structure of the XVIPCD of X-Tfe XAC2609 from Xanthomonas citri and to map its interaction surface with VirD4 AAD Isothermal titration calorimetry and in vivo Xanthomonas citri versus Escherichia coli competition assays using wild-type and mutant X-Tfe XAC2609 and X-Tfe XAC3634 indicate that XVIPCDs can be divided into two regions with distinct functions: the well-folded N-terminal region contains specific conserved motifs that are responsible for interactions with VirD4 AAD , while both N- and carboxyl-terminal regions are required for effective X-Tfe translocation into the target cell. The conformational stability of the N-terminal region is reduced at and below pH 7.0, a property that may facilitate X-Tfe unfolding and translocation through the more acidic environment of the periplasm.


  • Organizational Affiliation

    Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VirD4 interacting protein conserved domain105Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: XAC2609
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2017/17303-7
Sao Paulo Research Foundation (FAPESP)Brazil2018/09277-9

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references