SNAP output for PDB entry 7og0 [SNAP web server]

PDB-id

7og0; SNAP-derived features in text and JSON formats; DNAproDB

Class

peptide binding protein

Method

X-ray (2.61 Å)

Summary

Nontypeable haemophillus influenzae sapa in open and closed conformations, in complex with double stranded RNA

Reference

Lukacik P, Owen CD, Harris G, Bolla JR, Picaud S, Alibay I, Nettleship JE, Bird LE, Owens RJ, Biggin PC, Filippakopoulos P, Robinson CV, Walsh MA (2021): "The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif." Plos One, 16, e0256070. doi: 10.1371/journal.pone.0256070.

Abstract

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 (Kd 282 μM) through a surface exposed histidine, while the dsRNA is coordinated via residues which constitute part of a conserved motif (estimated Kd 4.4 μM). 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.