Resonance Raman (RR) and "light" minus "dark" Fourier transform infrared (FTIR) difference spectra are reported for the CO-bound caa(3) oxidase from Thermus thermophilus. Two Fe-CO stretching modes at 518 and 507 cm(-1), the Fe-C-O bending mode at 570 cm(-1), and three C-O modes of heme a(3) at 1958, 1967, and 1973 cm(-1) have been identified in the RR and FTIR spectra, respectively. The FTIR "light" minus "dark" spectrum indicates the formation of CuBCO as revealed by its nu(CO) at 2060/2065 cm(-1). We assign the bands at 518 (nu(Fe-CO)) and 1967/1973 cm(-1) (nu(C-O)) as the alpha-conformation. We also assign the bands at 507 and 1958 cm(-1) (nu(C-O)) as originating from the beta-conformation of the enzyme. A frequency upshift of the heme a3 Fe-His mode is observed subsequent to CO photolysis from 209 cm(-1) in the equilibrium deoxy enzyme to 214 cm(-1) in the photoproduct. The caa(3) data, distinctly different from those of ba(3) oxidase, are discussed in terms of the coupling of the alpha- and beta-conformations that occur in heme-copper oxidases with catalytic function. The dynamics between the heme a(3) and heme a propionates as revealed by the perturbation of the bending vibrations 6 prop of hemes a and a(3) at 385 and 392 cm(-1), respectively, induced upon CO binding to heme a(3) is discussed in terms of the protonic connectivity between the heme a ring-D propionate/Arg site with that of the heme a(3) ring-D propionate-H2O site that leads to the highly conserved in the heme-copper oxidases water pool.