Sensing preferences for prokaryotic solute binding protein families

Abstract

Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three‐dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron‐chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.

Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides

“…The SBP superfamily is a large group of proteins (>3.4 million sequences in February 2024) , with diverse sequences and ligand-binding preferences. , Although SBPs share a common core architecture comprising two primary α/β domains linked by a flexible hinge region and a central ligand-binding cleft, their structures are diverse and cover 33 distinct Pfam structural families . Proteins of the “extracellular solute-binding protein, family 5” Pfam family (“SBP_bac_5,” PF00496) are among the most structurally divergent SBPs and contain three topological domains .…”

“…13,18 Although SBPs share a common core architecture comprising two primary α/β domains linked by a flexible hinge region and a central ligand-binding cleft, their structures are diverse and cover 33 distinct Pfam structural families. 19 Proteins of the "extracellular solute-binding protein, family 5" Pfam family ("SBP_bac_5," PF00496) are among the most structurally divergent SBPs and contain three topological domains. 13 Unlike other structural classes of SBPs, which show preferences for a particular ligand class, 19 members of the SBP_bac_5 family bind a range of ligand types, including oligopeptides, 20,21 glutathione, 22,23 and metal ions.…”

Control of Biofilm Formation by anAgrobacterium tumefaciensPterin-Binding Periplasmic Protein Conserved Among Pathogenic Bacteria

“…Alpha Fold predictions suggests that the DcpA periplasmic domain forms a novel four helix CACHE-type bundle, with overall structural similarity to the four helix bundles in the periplasmic domains of methyl-accepting dependent chemotaxis proteins (MCPs), that impart chemotactic motility responses to certain solutes (35). Rather than interacting directly with their ligands in the periplasm, several MCPs mediate the response through interactions with periplasmic solute binding proteins (SBPs) (36). The interaction of PruR and the DcpA periplasmic domain may share similarities with MCP-SBP interactions, with binding of the pterin fostering this interaction.…”

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

“…The SBP superfamily is a large group of proteins (> 3.4 million sequences in February 2024) (16,17) with diverse sequences and ligand-binding preferences (13,18). Although prokaryotic SBPs share a common core architecture comprising two primary α/β domains linked by a flexible hinge region and a central ligand-binding cleft, their structures are diverse and cover 33 distinct Pfam structural families (19). Proteins of the "extracellular solute-binding protein, family 5" Pfam family ("SBP_bac_5", PF00496) are amongst the most structurally divergent SBPs and contain three topological domains (13).…”

“…Proteins of the “extracellular solute-binding protein, family 5” Pfam family (“SBP_bac_5”, PF00496) are amongst the most structurally divergent SBPs and contain three topological domains (13). Unlike other structural classes of SBPs, which show preferences for a particular ligand class (19), members of the SBP_bac_5 family bind a range of ligand types, including oligopeptides (20,21), glutathione (22,23) and metal ions (24,25). While a handful of the SBP_bac_5 proteins have been experimentally characterized, much of the sequence and functional diversity of the SBP_bac_5 family remains unexplored.…”