Structural basis of coiled-coil domain-mediated inhibition of A. baumannii AbTir NAD+ nucleosidase activity

Abstract

TIR (Toll/interleukin-1 receptor) domains are central components of innate immunity and cell-death pathways across diverse forms of life. In bacteria, TIR domain-containing proteins participate in diverse antiphage defence systems, several of which rely on NADase activity carried out by TIR domains. This nucleosidase activity is often regulated by additional domains that modulate activation and specificity in response to infection. AbTir, a TIR domain-containing protein from Acinetobacter baumannii, contains an N-terminal CC domain that negatively regulates its NADase activity, but the structural basis of this regulation remains unknown. Here, we used X-ray crystallography to investigate the molecular basis of CC domain-mediated regulation in AbTir. We determined the crystal structure of full-length AbTir in complex with a nanobody, revealing a symmetric AbTir TIR dimer in which only one of the two symmetry-related CC helices is accommodated at the dimer surface, breaking the overall symmetry of the full-length protein. Structural comparisons with other bacterial TIR domains suggest that such TIR dimers likely represent an inactive state, in which the NAD+-binding site has not yet formed. Phylogenetic analysis places AbTir within a family of bacterial TIR proteins associated with defence-related genomic loci, although phage-spot assays performed in the surrogate host Escherichia coli did not detect measurable antiphage activity. Together, these findings reveal an unusual structural mechanism of CC domain-mediated inhibition of a bacterial TIR NADase and expand our understanding of the mechanistic diversity of bacterial TIR proteins.