3HB3

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase

Summary for 3HB3

• Entry DOI: 10.2210/pdb3hb3/pdb
• Related: 1AR1
• Descriptor: Cytochrome c oxidase subunit 1-beta, DODECYL-BETA-D-MALTOSIDE, HYDROGEN PEROXIDE, ... (12 entities in total)
• Functional Keywords: electron transfer, proton transfer, proton pumping, membrane protein, cell inner membrane, cell membrane, copper, disulfide bond, electron transport, heme, hydrogen ion transport, ion transport, iron, membrane, metal-binding, oxidoreductase, respiratory chain, transmembrane, transport, pyrrolidone carboxylic acid
• Biological source: Paracoccus denitrificans; More
• Cellular location: Cell inner membrane; Multi-pass membrane protein: P98002 P08306
• Total number of polymer chains: 4
• Total formula weight: 134103.98

Authors

Koepke, J.,Angerer, H.,Peng, G. (deposition date: 2009-05-04, release date: 2009-06-23, Last modification date: 2024-11-27)

Primary citation

Koepke, J.,Olkhova, E.,Angerer, H.,Muller, H.,Peng, G.,Michel, H.
High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways
Biochim.Biophys.Acta, 1787:635-645, 2009

PubMed Abstract: 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.

PubMed: 19374884
DOI: 10.1016/j.bbabio.2009.04.003

Experimental method

X-RAY DIFFRACTION (2.25 Å)