Structural insights into a putative BLF1-like deamidase from Methylomonas sp. Kb3

Bacteria that act as eukaryotic pathogens are known to express enzyme toxins that interfere with critical pathways in their targets. Among these are deamidases that modify conserved glutamine residues such as those found in eukaryotic initiation factor 4A (eIF4A) or in the small GTPases Rho, Rac and Cdc42, converting them to glutamic acid and thereby disrupting the function of the target proteins. Structural and biochemical studies have shown that deamidases from Burkholderia, Burkholderia lethal factor 1 (BLF1), and from Escherichia coli, cytotoxic necrotizing factor (CNF1), share a similar fold in their deamidase domains with similar mechanisms for deamidase chemistry. The active site of these toxins contains an apparently conserved LSGC motif as part of a cysteine-histidine catalytic dyad which catalyses the site-specific deamidation. Sequence searches in bacterial databases have suggested that deamidases with this fold are more widespread in nature and that the LSGC motif varies substantially. Using crystals grown in magnesium sulfate, we determined the 1.95 Å resolution crystal structure of a putative deamidase from Methylomonas sp. Kb3, CWO84_RS12955, which shows limited sequence identity to BLF1. The structure reveals that CWO84_RS12955 adopts a similar fold to that of BLF1, albeit with significant differences at the periphery due to sequence insertions and deletions, and that it conserves the catalytic dyad but replaces the LSGC motif with MDGC. However, compared with BLF1, none of the residues that interact with eIF4A are conserved. These structural features suggest that the Methylomonas protein that we have identified may act as a BLF1-like deamidase but against a currently unknown target, and that other bacterial proteins with similar sequence fingerprints could play important roles in broader bacterial biology.