6K94

Crystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri - a 70 residue N-terminal truncation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Crystal Structure-Based Exploration of Arginine-Containing Peptide Binding in the ADP-Ribosyltransferase Domain of the Type III Effector XopAI Protein.

Liu, J.H., Yang, J.Y., Hsu, D.W., Lai, Y.H., Li, Y.P., Tsai, Y.R., Hou, M.H.

(2019) Int J Mol Sci 20

  • DOI: 10.3390/ijms20205085
  • Primary Citation of Related Structures:  
    6K93, 6K94, 6KLY

  • PubMed Abstract: 

    • Plant pathogens secrete proteins called effectors into the cells of their host to modulate the host immune response against colonization. Effectors can either modify or arrest host target proteins to sabotage the signaling pathway, and therefore are considered potential drug targets for crop disease control ...

    Plant pathogens secrete proteins called effectors into the cells of their host to modulate the host immune response against colonization. Effectors can either modify or arrest host target proteins to sabotage the signaling pathway, and therefore are considered potential drug targets for crop disease control. In earlier research, the Xanthomonas type III effector XopAI was predicted to be a member of the arginine-specific mono-ADP-ribosyltransferase family. However, the crystal structure of XopAI revealed an altered active site that is unsuitable to bind the cofactor NAD+, but with the capability to capture an arginine-containing peptide from XopAI itself. The arginine peptide consists of residues 60 through 69 of XopAI, and residue 62 (R62) is key to determining the protein-peptide interaction. The crystal structure and the molecular dynamics simulation results indicate that specific arginine recognition is mediated by hydrogen bonds provided by the backbone oxygen atoms from residues W154, T155, and T156, and a salt bridge provided by the E265 sidechain. In addition, a protruding loop of XopAI adopts dynamic conformations in response to arginine peptide binding and is probably involved in target protein recognition. These data suggest that XopAI binds to its target protein by the peptide-binding ability, and therefore, it promotes disease progression. Our findings reveal an unexpected and intriguing function of XopAI and pave the way for further investigation on the role of XopAI in pathogen invasion.

    Organizational Affiliation: 

    PhD Program in Medical Biotechnology, NCHU, Taichung 40227, Taiwan. mhho@nchu.edu.tw.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type III effector XopAIA, B, C, D247Xanthomonas citriMutation(s): 0 
Gene Names: XopAI, XAC3230
EC: 2.4.2.31
UniProt
Find proteins for Q8PHM1 (Xanthomonas axonopodis pv. citri (strain 306))
Explore Q8PHM1 
Go to UniProtKB:  Q8PHM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PHM1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.78α = 90
b = 98.76β = 91.21
c = 77.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)TaiwanMOST 106-2313-B-005-029

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release