IA and OM were supported by the Deutsche Forschungsgemeinschaft (SFB 749, project C08; and CIPSM)

IA and OM were supported by the Deutsche Forschungsgemeinschaft (SFB 749, project C08; and CIPSM). MMP, DWW, NM, RPM and GS devised the study. search for such inhibitors has remained challenging (McGeary et al., 2017). MBLs are divided into three subgroups, i.e. B1, B2 and B3 (Bush and Jacoby, 2010). Enzymes of the B1 subgroup constitute the majority of MBLs associated with antibiotic resistance (Khan et al., 2017). Fewer B2-type MBLs are currently known; they are phylogenetically related to B1 MBLs but are characterized by a preference for last line carbapenem substrates (Sun et al., 2016). While B3-type MBLs share low sequence similarity to B1 and B2 enzymes Vandetanib HCl ( ?20% amino acid (aa) identity), they have a substrate range similar to that of B1 MBLs (Selleck et al., 2016; Lee et al., 2019). MBLs contain catalytic centres that can accommodate two closely spaced Zn2+ ions bound in the and sites with similar yet distinct sequence motifs (B1: His116, His118, His196 and Asp120, Cys221, His263 (i.e., HHH/DCH) for the and sites, respectively; B2: NHH/DCH; B3: HHH/DHH). For B3-type MBLs two variations of the canonical active site motif have been observed, QHH/DHH in GOB-1/18 from the opportunistic pathogen and HRH/DQK in SPR-1 from (variations shown in bold) (Vella et al., 2013; Moran-Barrio et al., 2016). The discovery of atypical active sites in B3-type MBLs may have important implications for the design of clinically useful MBL inhibitors. We thus probed the evolutionary history and diversity of B3-type MBLs by searching for homologs in the release 02-RS83 of the Genome Taxonomy Database (Parks et al., 2018) comprising 111,330 quality-filtered bacterial and archaeal genomes. A total of 1 1,449 B3 MBL proteins were identified in 1,383 genomes (representing 1.2% of all analyzed genomes), of which 1,150 have the characteristic B3 active site residues (HHH/DHH), 162 the QHH/DHH and 47 the HRH/DQK motifs. In addition, we also discovered 90 proteins with another single aa variation in the -site (EHH/DHH). Phylogenetic inference of a representative subset of 761 of these proteins indicates that each of the three motif variants originate from within the B3 radiation when using Class D SBLs as the outgroup (Fig.?1). We therefore propose to use the active site aa changes as a means of distinguishing the variants (i.e., B3-RQK, B3-Q, B3-E). B3-RQK appears to have only arisen once, likely because the ancestral change required at least four nucleotide (nt) substitutions to produce the three aa changes. By contrast, the B3-Q and B3-E variants have a single aa difference in position 116 requiring only one and two nt changes, respectively. The B3-Q variant appears to have arisen on at least six independent occasions and reverted back to the B3 motif on at least three occasions as a result of the need for only one nt change. Open in a separate window Figure 1 Maximum likelihood tree Rabbit polyclonal to CLIC2 of MBLs belonging to subgroup B3, highlighting three active site variants. The tree was inferred from 688 dereplicated B3 MBLs identified in 1,383 bacterial genomes screened from a total of 111,330 bacterial and archaeal genomes. Bootstrap support for the interior nodes is indicated Vandetanib HCl by filled (black: ?90%, gray: ?80%) Vandetanib HCl or open ( ?70%) circles. Representatives of class D SBLs were used as an outgroup for the analysis (not shown). B3 active site variants are indicated by different colors according to the legend in the top left of the figure. The inner circle (1) represents the phylum-level affiliations of the B3-containing bacteria. The middle circle (2) represents the habitat. Source of the B3-containing bacteria, and the outer circle (3) represents B3 gene copy number in each genome No archaeal genomes harbored B3-type MBLs, and the majority.