7OG0 image
Entry Detail
PDB ID:
7OG0
Title:
Nontypeable Haemophillus influenzae SapA in open and closed conformations, in complex with double stranded RNA
Biological Source:
PDB Version:
Deposition Date:
2021-05-05
Release Date:
2021-10-27
Method Details:
Experimental Method:
Resolution:
2.61 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
Chain IDs:A, B
Chain Length:527
Number of Molecules:2
Biological Source:Haemophilus influenzae (strain 86-028NP)
Polymer Type:polyribonucleotide
Description:RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
Chain IDs:C (auth: D), D (auth: E)
Chain Length:17
Number of Molecules:2
Biological Source:Escherichia coli
Ligand Molecules
Primary Citation
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 e0256070 (2021)
PMID: 34653190 DOI: 10.1371/journal.pone.0256070

Abstact

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.

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Primary Citation of related structures