Identification and characterization of a bacterial periplasmic solute binding protein that binds L-amino acid amides

Abstract

Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP fromMesorhizobiumsp. A09 (MeAmi_SBP) and show thatMeAmi_SBP bindsl-amino acid amides but not the correspondingl-amino acids. An X-ray crystal structure ofMeAmi_SBP bound tol-serinamide highlights the residues that impart distinct specificity forl-amino acid amides and reveals a structural Ca2+binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca2+binding are conserved amongst the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake and metabolism ofl-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose thatMeAmi_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions withl-amino acid amides and bacterial nitrogen utilization.