Resonance Raman spectra and excitation profiles (413-676 nm) are reported for four distinct forms of Rhodobacter sphaeroides dimethyl sulfoxide (DMSO) reductase: as prepared Mo(VI), dithionite-reduced Mo(IV), dimethyl sulfide reduced Mo(IV), and glycerol-inhibited Mo(V). All of the vibrational modes in the 200-1700 cm(-1) region of the Mo(VI) and Mo(IV) forms are assigned to vibrations involving atoms in the first or second coordination sphere of the bis-molybdopterin-coordinated Mo active site, the dithiolene chelate rings, or nonresonantly enhanced protein modes. On the basis of O-18/O-16 isotope shifts, the Mo(VI) form is shown to be mono-ore with nu(Mo=O) at 862 cm(-1), and the DMS-reduced Mo(IV) form is shown to involve bound DMSO with nu(Mo-O) at 497 cm(-1) and nu(S=O) at 862 cm(-1). Bands at 536 and 513 cm(-1) are tentatively assigned to nu(Mo-O(Ser)) stretching modes of coordinated serinate in the Mo(VI) and Mo(IV) forms, respectively. The vibrational modes of two distinct types of dithiolene chelate rings are identified on the basis of their excitation profiles, and the frequencies indicate that one is best viewed as a dithiolate ligand, while the other has more pi-delocalized character. In the low-frequency region between 335 and 405 cm(-1), the Mo-S stretching modes of a distorted square pyramidal MoS4 unit are assigned in each of the four derivatives investigated, based on the S-34 isotope shifts and sensitivity to Mo oxidation state. The average Mo-S bond strength increases with decreasing Mo oxidation state. Taken together, the Mo-S and dithiolene vibrational assignments indicate that all four of the molybdopterin dithiolene S atoms remain coordinated in each of the four forms investigated. Structures for each of these four derivatives are proposed on the basis of the resonance Raman results, and the ability to monitor directly the origin and fate of the Mo oxo group via isotopic labeling indicates that each corresponds to a catalytically competent intermediate in the reaction cycle. Overall, the results provide direct confirmation of an oxygen atom transfer mechanism, with the active site cycling between mono-oxo-Mo(VI) and des-oxo-Mo(IV) forms via a DMSO-bound Mo(IV) intermediate, and the molybdopterin dithiolene ligands staying firmly attached throughout the catalytic cycle.