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

DOI: 10.1371/journal.pone.0256070 DOI Help

Authors: Petra Lukacik (Diamond Light Source) , C. David Owen (Diamond Light Source) , Gemma Harris (Research Complex at Harwell) , Jani Reddy Bolla (University of Oxford) , Sarah Picaud (Structural Genomics Consortium, University of Oxford) , Irfan Alibay (University of Oxford) , Joanne E. Nettleship (Research Complex at Harwell; Wellcome Trust Centre for Human Genetics, University of Oxford) , Louise E. Bird (Research Complex at Harwell; Wellcome Trust Centre for Human Genetics, University of Oxford) , Raymond Owens (Research Complex at Harwell; Wellcome Trust Centre for Human Genetics, University of Oxford) , Philip C. Biggin (University of Oxford) , Panagis Filippakopoulos (Structural Genomics Consortium, University of Oxford) , Carol V. Robinson (University of Oxford) , Martin A. Walsh (Diamond Light Source)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Plos One , VOL 16

State: Published (Approved)
Published: October 2021
Diamond Proposal Number(s): 4990 , 5073 , 4988

Open Access Open Access

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.

Journal Keywords: Heme; Crystal structure; Crystals; Escherichia coli; RNA structure; Ribosomal RNA; Crystallization; Protein domains

Diamond Keywords: Bacteria

Subject Areas: Biology and Bio-materials

Instruments: I04-1-Macromolecular Crystallography (fixed wavelength) , I04-Macromolecular Crystallography

Added On: 18/10/2021 11:31


Discipline Tags:

Pathogens Antibiotic Resistance Infectious Diseases Health & Wellbeing Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)