Ligninase Activity Is Not Consistently Predicted by the Presence of Manganese Coordinating Residues in Dyp-like Proteins

DypB, a characterized bacterial lignin peroxidase from Rhodococcus jostii RHA1, is thought to modify lignin using oxidized manganese as a diffusible mediator. Structural analysis has determined that manganese is bound and oxidized through a pocket near the active site that is comprised of four residues. This study aimed to experimentally determine whether the manganese coordinating chemistry of DypB could be predictive of manganese oxidation activity and lignin modification of other dyp-like proteins. To do so a dyp-like protein from Pseudomonas putida F1 was cloned and its manganese oxidizing potential determined. Moreover, the ability to grow in the presence of lignin was also determined for seven environmental isolates which were predicted to contain dyp-like proteins of interest. The results suggest that the conservation of key residues responsible for manganese oxidation in DypB are not directly indicative of lignin modification. This study also found that a novel Enterobacter sp. and Streptomyces viridochromogenes DSM40736 may utilize lignin in a manner comparable to and greater than R. jostii RHA1.