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In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function

Abstract

Bacterial acetyltransferase effectors belonging to the Yersinia outer protein J (YopJ) group inhibit multiple immune signaling pathways in human and plants. The present study determines in-silico acetyl-coenzyme A (AcCoA) binding and Arabidopsis immune regulator RPM1-interacting protein4 (RIN4) peptide interactions to YopJ effector hypersensitivity and pathogenesis-dependent outer proteinZ3 (HopZ3) from Pseudomonas syringae. Phylogenetic analysis revealed that HopZ3 was clustered by acetyltransferase effectors from plant bacterial pathogens. Structural juxtaposition shows HopZ3 comprises topology matched closer with HopZ1a than PopP2 effectors, respectively. AcCoA binds HopZ3 at two sites i.e., substrate binding pocket and catalytic site. AcCoA interactions to substrate binding pocket was transient and dissipated upon in-silico mutation of Ser 279 residue whereas, attachment to catalytic site was found to be stable in the presence of inositol hexaphosphate (IP6) as a co-factor. Interface atoms used for measuring hydrogen bond distances, bound or accessible surface area, and root-mean-square fluctuation (RMSF) values, suggests that the HopZ3 complex stabilizes after binding to AcCoA ligand and RIN4 peptide. The few non-conserved polymorphic residues that have been displayed on HopZ3 surface presumably confer intracellular recognitions within hosts. Collectively, homology modeling and interactive docking experiments were used to substantiate Arabidopsis immune ‘guardee’ interactions to HopZ3.

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JC conceptualized and performed the research. JC wrote the manuscript.

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Correspondence to Joydeep Chakraborty.

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Chakraborty, J. In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function. J Plant Res 134, 599–611 (2021). https://doi.org/10.1007/s10265-021-01274-8

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Keywords

  • Acetylation
  • Effector
  • Ligand
  • Molecular docking
  • Substrate