Fig. 3: Structural basis of the MCPDRK chemoreceptor binding d-Arg and d-Lys.
From: d-amino acids signal a stress-dependent run-away response in Vibrio cholerae
a, Domain architecture of MCPDRK protein generated by alphafold40,41,42, showing one subunit in rainbow colours, with the N terminus in blue and C terminus in red. The full-length MCPDRK transmembrane chemoreceptor contains a ligand binding ___domain (LBD), a transmembrane (TM) and a signalling ___domain. b, MCPDRK-LBD monomers bound to d-Arg (purple spheres) or d-Lys (orange spheres) are coloured in rainbow colours from the N terminus (blue) to the C terminus (red). c, Superimposition of the LBD ___domain of MCPDRK crystallized with d-Arg (in purple) and d-Lys (in orange) with the aspartate-bound Tar receptor from E. coli (PDB ID: 4z9i in green)81, the citrate bound MCP2201 chemoreceptor from C. testosterone (PDB ID: 5XUB, in blue)34 and the more promiscuous quinate-bound PcaY_PP chemoreceptor from P. putida (PDB ID: 6S38, in yellow)35. The Tar and the PcaY_PP receptor ligand binding sites are located at the dimer interface and are therefore shown as dimers. d, The binding site of MCPDRK-LBD bound to d-Arg (in purple). e, The binding site of MCPDRK-LBD bound to d-Lys (in orange). f, Functional analysis of the d-Arg binding pocket was performed by substituting residues Asn43, Asp47, Thr48, Thr105, W107, Glu111 and Asn176 with an alanine. Chemotactic response to d-Arg was then analysed for ΔmcpDKR cells expressing either wild-type or mutant MCPDRK under its native promoter. ΔbsrV strain was used as background. −, not complemented ΔmcpDRK. Black diamonds represent the mean of 3 independent biological replicates. Significant differences (unpaired t-test) are indicated by *P < 0.05 or **P < 0.01.
