Structure-function analysis indicates that an active site water participates in dimethylsulfoniopropionate cleavage by DddK.

The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei, and thus may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria, many of which contain the DMSP lyase DddK and whose dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the β-elimination reaction of DMSP. This Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its' neighboring His96. To further probe into this mechanism, we purified and characterized the same DddK protein from Pelagibacter ubique HTCC1062 and determined the crystal structures of wild type DddK, and mutants Y64A and Y122A, where the latter is complexed with DMSP. Structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its' deprotonation. Our data indicates an active water in the active site of DddK plays an important role in the deprotonation of Tyr64, and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding on DMS generation by SAR11 bacteria. Importance The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which forms cloud condensation nuclei that influence the reflectivity of clouds and thereby global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, many of which contain DMSP lyase DddK to cleave DMSP generating DMS. In this study, we revealed the catalytic mechanism of DddK based on structural analyses and mutational assays, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.