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Publication Abstract from PubMed

In nontypeable Haemophilus influenzae (NTHi), the oligopeptide-binding protein OppA serves as the substrate-binding protein (SBP) responsible for peptide import. As a heme auxotroph, NTHi also uses host hemoproteins as an iron source. OppA is a member of the Cluster C SBP family, and unlike other SBP families, some members recognize two distinctly different substrates. DppA (dipeptide), MppA (murein tripeptide), and SapA (antimicrobial peptides) are Cluster C proteins known to also transport heme. However, the ability of OppA to participate in heme binding and how Cluster C proteins accommodate these heme and peptide substrates are unclear. Here, we solved the crystal structure of nthiOppA in complex with hydrophobic peptides of various sizes. The hexapeptide complex revealed the flexibility of nthiOppA's binding cavity to expand and accommodate a longer peptide substrate while maintaining similar protein-peptide interactions used to bind smaller peptides. Additionally, we observed the multifunctional heme binding of nthiOppA, and using surface plasmon resonance (SPR), we established heme specificity and affinity of the four Cluster C proteins in NTHi. Ligand-docking studies predicted a distinct heme-specific cleft in the nthiOppA substrate-binding pocket, and SPR competition assays confirmed that heme does not directly compete with peptides in this pocket. Additionally, we noted that the individual nthiOppA domains differentially contribute to substrate binding, with one domain playing a dominant role in heme binding and the other in peptide binding. Our results identified multi-substrate specificity of nthiOppA and distinguished the roles of NTHi Cluster C proteins in the heme-uptake pathway of this bacterial pathogen.

Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket.,Tanaka KJ, Pinkett HW J Biol Chem. 2018 Nov 19. pii: RA118.004479. doi: 10.1074/jbc.RA118.004479. PMID:30455346^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.