The direct oxygen sensor protein from Escherichia coli (Ec DOS) is a heme-based signal transducer protein responsible for phosphodiesterase (PDE) activity. Binding of either O-2 or CO molecule to a reduced heme enhances the PDE activity toward 3',5'-cyclic diguanylic acid. We report ultraviolet resonance Raman (UVRR) spectroscopic investigations of the reduced, O-2- and CO-bound forms of heme-bound PAS domain of Ec DOS. The UVRR results show that heme discriminates different ligands, resulting in altered conformations in the protein moiety. Specifically, the environment around Trp53 that contacts the 2-vinyl group of heme, is changed to a more hydrophobic environment by O-2 binding, whereas it is changed to a more hydrophilic environment by CO-binding. In addition, the PDE activity of the O-2- and CO-bound forms for the Trp53Phe mutant is significantly decreased compared with that of the wild type (WT), demonstrating the importance of Trp53 for the catalytic reaction. On the other hand, the binding of O-2 or CO to the heme produces drastic changes in the Tyr126 of I-beta-strand at the surface of the sensor domain. Furthermore, we found that Asn84 forms a hydrogen bond with Tyr126 either in the O-2- or CO-bound forms but not in the reduced form. Finally, the PDE activities of the ligand-bound forms for Asn84Val and Tyr126Phe mutants are significantly reduced as compared with that of WT, suggesting the importance of the hydrogen-bonding network from heme 6-propionate to Tyr126 through Asn84 in signal transmission.