Fig. 2: Interaction surface of PdeB and HubP.
From: GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP
a, b Regions that are involved in the interaction of PdeB and HubP were identified using HDX-MS (a) and CL-MS (b). The sequences of SpHubP and SoHubP were aligned using clustal omega and JalView. c The structure of the C-terminal domain of SpHubP was predicted using the swiss-model algorithm and the peptide found by CL-MS is colored in orange. d The electrostatic surface potential was calculated using the APBS electrostatic tool and pymol. Red coloring indicates a negative surface charge. e The structure of the PAS-GGDEF-EAL region of PdeB was predicted using Phyre2. The N-terminal PAS domain is colored in gray, the GGDEF domain in green and the C-terminal EAL domain in light orange. Residues within the GGDEF domain that we identified to be involved in the PdeB-HubP interaction are colored in cyan. f The dissociation constant for the SoPdeB-SoHubP interaction was determined using BLI assays. The specific binding in nanometer was determined by subtracting the unspecific binding of the analyte in absence of the ligand FimV. g–k Residues that are involved in respective interaction were substituted as indicated and the KD value was determined using BLI assays. All mutations decreased the affinity of SoGGDEF to SoFimV.
