Identification and description of copper-thiolate vibrations in the dinuclear Cu-A site of cytochrome c oxidase

The Cu-A site of cytochrome c oxidase and the type 1 Cu site of cupredoxins occur in homologous protein fords with a His(2)Cys ligand set, but the distinguished by the presence of a second Cys and a second Cu in Cu-A that result in the formation of a dithiolate-bridged dinuclear Cu cluster. The resonance Raman (RR) spectrum of the soluble Cu-A-containing fragment from Paracoccus denitrificans exhibits intense vibrations at 260 and 339 cm(-1). Their respective S-34-isotope shifts of -4.1 and -5.1 cm(-1) allow them to be assigned to two Cu-S stretching modes, nu(Cu-S), of the Cu(2)S(2)Im(2) moiety. A normal coordinate analysis (NCA) of the RR spectra of Cu-A substituted with isotopes of S, Cu, and N was carried out to determine whether it is possible to distinguish between dinuclear models with bridging or terminal cysteine ligands. Whereas the terminal Cys model predicts that both of the nu(Cu-S) modes lie between 340 and 350 cm(-1). the bridging Cys geometry successfully predicts the S-shifts at 260 and 339 cm(-1). Thus, the Raman data and NCA are fully consistent with the bridging cysteine coordination observed by X-ray crystallography. The agreement between predicted and observed vibrational isotope data is further improved by a trans-tilting of the imidazole nitrogens above and below the Cu2S2 plane, yielding a distorted tetrahedral geometry fur each of the Cu atoms. Whereas type I protein RR spectra are highly N-dependent due to extended vibronic coupling with 1 amide vibrations of the cysteine ligand, the vibrations in CUA are relatively insensitive to N-isotope substitution. Thus, unlike type 1 Cu, the RR spectrum of CUA can be successfully modeled with only the Cu2S2-(Im)(2) core.