High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways.
The structure of the two-subunit cytochrome c oxidase from Paracoccus denitrificans has been refined using X-ray cryodata to 2.25 A resolution in order to gain further insights into its mechanism of action. The refined structural model shows a number of new features including many additional solvent and detergent molecules. The electron density bridging the heme a(3) iron and Cu(B) of the active site is fitted best by a peroxo-group or a chloride ion. Two waters or OH(-) groups do not fit, one water (or OH(-)) does not provide sufficient electron density. The analysis of crystals of cytochrome c oxidase isolated in the presence of bromide instead of chloride appears to exclude chloride as the bridging ligand. In the D-pathway a hydrogen bonded chain of six water molecules connects Asn131 and Glu278, but the access for protons to this water chain is blocked by Asn113, Asn131 and Asn199. The K-pathway contains two firmly bound water molecules, an additional water chain seems to form its entrance. Above the hemes a cluster of 13 water molecules is observed which potentially form multiple exit pathways for pumped protons. The hydrogen bond pattern excludes that the Cu(B) ligand His326 is present in the imidazolate form.
Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue-Str.3, D-60438 Frankfurt/Main, Germany.
Juergen
J
Koepke
Elena
E
Olkhova
Heike
H
Angerer
Hannelore
H
Müller
Guohong
G
Peng
Hartmut
H
Michel
D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003576:Electron Transport Complex IV / Q000737:chemistry* / Q000378:metabolism*; D006418:Heme / Q000737:chemistry; D006860:Hydrogen Bonding; D008954:Models, Biological; D008958:Models, Molecular; D010231:Paracoccus denitrificans / Q000201:enzymology*; D011487:Protein Conformation; D011522:Protons; D055672:Static Electricity; D014867:Water / Q000737:chemistry
D001426:Bacterial Proteins; D011522:Protons; D014867:Water; D006418:Heme; D003576:Electron Transport Complex IV