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 from Mesorhizobium sp. A09 ( Me Ami_SBP) and show that Me Ami_SBP binds l -amino acid amides but not the corresponding l -amino acids. An X-ray crystal structure of Me Ami_SBP bound to l -serinamide highlights the residues that impart distinct specificity for l -amino acid amides and reveals a structural Ca 2+ binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca 2+ 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 of l -amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that Me Ami_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 with l -amino acid amides and bacterial nitrogen utilization.