The family of S1-P1 nucleases contains zinc-dependent 3'-nucleases/nucleotidases cleaving phosphodiester bond of nucleic acids. Gene coding an S1-P1 type nuclease can be found in many species. In plants and fungi (i.e. TBN1 nuclease from Solanum lycopersicum, S1 nuclease from Aspergillus oryzae), these nucleases were already functionally and structurally well characterized [1, 2], but the potential role of their homologs from bacteria or protozoan parasites is not fully understood and their crystal structure is yet to be determined. As they occur in some opportunistic human pathogens (i.e. Legionella pneumophila, Leishmania major), they became an interesting target for biomedical and biotechnology studies [3].
Here we present crystal structures of recombinant class I nuclease from Stenotrophomonas maltophilia (SmNuc1), structure of the native enzyme at 1.4 Å resolution and two crystal structures with 5-mononucleotides present in the active site. Stenotrophomonas maltophilia is Gram-negative aerobic bacterium from Gammaproteobacteria. It is a human opportunistic pathogen which causes several nosocomial diseases and has high multidrug resistance. SmNuc1 nuclease is a 28 kDa protein, composed mostly of α-helices with two disulfide bridges. The active site composition and protein fold are similar to its eukaryotic homologs, but there are some differences in the surface properties and substrate binding site.
Based on these new structures, we are able to suggest mutations of some specific sites. These mutations could help us fully understand the substrate-binding mechanism, which could lead to specific inhibitors for S1‑P1 type nucleases from bacterial pathogens.
This work was supported by the project CIISB4HEALTH (CZ.02.1.01/0.0/0.0/16_013/0001776) and by the project Structural dynamics of biomolecular systems (CZ.02.1.01/0.0/0.0/15_003/0000447) from the ERDF, by MEYS CR (LM2015043 CIISB) and also from specific university research (MSMT No 21-SVV/2020) .