3FYE

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state

Summary for 3FYE

• Entry DOI: 10.2210/pdb3fye/pdb
• Related: 2GSM 3FYI
• Descriptor: Cytochrome C oxidase subunit 1, HEPTANE-1,2,3-TRIOL, CADMIUM ION, ... (12 entities in total)
• Functional Keywords: conformational changes, cell membrane, copper, electron transport, heme, hydrogen ion transport, ion transport, iron, membrane, metal-binding, respiratory chain, transmembrane, transport, oxidoreductase
• Biological source: Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides); More
• Cellular location: Cell membrane; Multi-pass membrane protein: P33517 Q03736
• Total number of polymer chains: 4
• Total formula weight: 196678.72

Authors

Qin, L.,Mills, D.A.,Proshlyakov, D.A.,Hiser, C.,Ferguson-Miller, S. (deposition date: 2009-01-22, release date: 2009-06-16, Last modification date: 2023-09-06)

Primary citation

Qin, L.,Liu, J.,Mills, D.,Proshlyakov, D.A.,Hiser, C.,Ferguson-Miller, S.
Redox dependent conformational changes in cytochrome c oxidase suggest a gating mechanism for proton uptake.
Biochemistry, 48:5121-5130, 2009

PubMed Abstract: A role for conformational change in the coupling mechanism of cytochrome c oxidase is the subject of controversy. Relatively small conformational changes have been reported in comparisons of reduced and oxidized crystal structures of bovine oxidase but none in bacterial oxidases. Comparing the X-ray crystal structures of the reduced (at 2.15 A resolution) and oxidized forms of cytochrome c oxidase from Rhodobacter sphaeroides, we observe a displacement of heme a(3) involving both the porphyrin ring and the hydroxyl farnesyl tail, accompanied by protein movements in nearby regions, including the mid part of helix VIII of subunit I which harbors key residues of the K proton uptake path, K362 and T359. The conformational changes in the reduced form are reversible upon reoxidation. They result in an opening of the top of the K pathway and more ordered waters being resolved in that region, suggesting an access path for protons into the active site. In all high-resolution structures of oxidized R. sphaeroides cytochrome c oxidase, a water molecule is observed in the hydrophobic region above the top of the D path, strategically positioned to facilitate the connection of residue E286 of subunit I to the active site or to the proton pumping exit path. In the reduced and reduced plus cyanide structures, this water molecule disappears, implying disruption of proton conduction from the D path under conditions when the K path is open, thus providing a mechanism for alternating access to the active site.

PubMed: 19397279
DOI: 10.1021/bi9001387

Experimental method

X-RAY DIFFRACTION (2.15 Å)