8upi | pdb_00008upi
Structure of a periplasmic peptide binding protein from Mesorhizobium sp. AP09 bound to aminoserine
Structural highlights
FunctionA0A7R6WUD2_9HYPH Probably part of an ABC transporter complex that could be involved in peptide import.[ARBA:ARBA00037680] Publication Abstract from PubMedPeriplasmic 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 (MeAmi_SBP) and show that MeAmi_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of MeAmi_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 among 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 MeAmi_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. Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides.,Smith OB, Frkic RL, Rahman MG, Jackson CJ, Kaczmarski JA Biochemistry. 2024 May 21;63(10):1322-1334. doi: 10.1021/acs.biochem.4c00096. , Epub 2024 May 2. PMID:38696389[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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