Fig. 5: Phylogeny and homology modeling of the alpha subunit of biphenyl dioxygenase (BphA). | The ISME Journal

Fig. 5: Phylogeny and homology modeling of the alpha subunit of biphenyl dioxygenase (BphA).

From: Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses

Fig. 5

a BphA homologs from metagenomic bins are shown in bold font, and those affiliated to toluene/biphenyl dioxygenase (DO) are highlighted in red color. Filled circles on the tree branches indicated the bootstrap values >50%. The scale bar represents the number of substitutions per site. PAH-GN (GP): PAH dioxygenase from Gram-negative (Gram-positive) bacteria; T/B DO: toluene/biphenyl dioxygenase. b Sequence alignment of BphA from A_bin2, D_bin4, and well-known biphenyl degraders. Sequence regions that influenced the PCB congener preference and regiospecificity of biphenyl dioxygenase, are displayed [79, 80]. B. xenovorans: Burkholderia xenovorans; P. furukawaii: Pseudomonas furukawaii; C. testosteroni: Comamonas testosteroni. The amino acid numbering corresponds to BphA of the B. xenovorans LB400 sequence. c, Modeled substrate binding pocket in the BphA of D_bin4. The predicted BphA structure (yellow sticks) was superimposed on B. xenovorans BphA (blue wireline). The biphenyl molecule is shown as green lines.

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