CbpD crystal structure adds intrigue to substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases

Abstract

Pseudomonas aeruginosa secretes diverse proteins via its Type 2 Secretion System, including a 39 KDa Chitin-Binding Protein, CbpD. CbpD was recently shown to be a lytic polysaccharide monooxygenase active on chitin, and to contribute substantially to virulence. To-date no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the Cellvibrio japonicus CjLPMO10A CBM73 domain. We report the 3.0 Å resolution crystal structure of CbpD solved by molecular replacement, which required ab initio models of each CbpD domain generated by the artificial intelligence deep learning structure prediction algorithm RoseTTAFold. The structure of CbpD confirms previously postulated chitin-specific motifs in the AA10 domain while challenging the deterministic effects of other postulated substrate specificity motifs. Additionally, the structure of CbpD shows that post translational modifications occur on the chitin binding surface. Moreover, the structure raises interesting possibilities about how type 2 secretion system substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure prediction algorithms in making challenging structural targets tractable.

A novel lytic polysaccharide monooxygenase from enrichment microbiota and its application for shrimp shell powder biodegradation

“…Currently, increasing LPMOs are found to have multiple conserved domains, which play an essential role in the substrate binding and catalytic efficiency of LPMOs (Courtade and Aachmann, 2019;Mekasha et al, 2020). In addition, some domains may also protect LPMOs from autocatalytic inactivation (Dade et al, 2022). The analysis of conserved domains showed that M2822 contained four conserved domains (Figure 3C).…”