Conserved in both animal and plant pathogenic bacteria,SpvC belongs to a novel family of enzymes designated phosphothreonine lyase that irreversibly inactivate mitogen-activated protein kinases (MAPKs) to repress host innate immunity.Here we report the crystal structures of SpvC by itself and its complex with a substrate peptide.The structure reveals that the two phosphorylated residues in pThr-Xaa-pTyr motif predominantly mediate recognition of the peptide by SpvC.The methyl group of phosphothreonine contributes to substrate recognition by making Van der Waals contacts with two conserved residues from SpvC.