The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif

Nontypeable Haemophilus influenzae (NTHi) is a significant pathogen in respiratory disease and otitis media. Important for NTHi survival, colonization and persistence in vivo is the Sap (sensitivity to antimicrobial peptides) ABC transporter system. Current models propose a direct role for Sap in heme and antimicrobial peptide (AMP) transport. Here, the crystal structure of SapA, the periplasmic component of Sap, in a closed, ligand bound conformation, is presented. Phylogenetic and cavity volume analysis predicts that the small, hydrophobic SapA central ligand binding cavity is most likely occupied by a hydrophobic di- or tri- peptide. The cavity is of insufficient volume to accommodate heme or folded AMPs. Crystal structures of SapA have identified surface interactions with heme and dsRNA. Heme binds SapA weakly (K-d 282 mu M) through a surface exposed histidine, while the dsRNA is coordinated via residues which constitute part of a conserved motif (estimated K-d 4.4 mu M). The RNA affinity falls within the range observed for characterized RNA/protein complexes. Overall, we describe in molecular-detail the interactions of SapA with heme and dsRNA and propose a role for SapA in the transport of di- or tri-peptides.

Automated summary

The crystal structure of SapA, a component of the important Sap ABC transporter system in NTHi, has been found to be in a closed, ligand bound conformation, with its central ligand binding cavity likely occupied by di- or tri-peptides. Surface interactions between SapA and heme and dsRNA were observed, suggesting a potential role for SapA in the transport of di- or tri-peptides.