3BVD

Structure of Surface-engineered Cytochrome ba3 Oxidase from Thermus thermophilus under Xenon Pressure, 100psi 5min

Summary for 3BVD

• Entry DOI: 10.2210/pdb3bvd/pdb
• Related: 2qpd
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 2, Cytochrome c oxidase polypeptide 2A, ... (8 entities in total)
• Functional Keywords: cytochrome ba3 oxidase, heme, integral membrane protein, copper, electron transport, hydrogen ion transport, ion transport, iron, metal-binding, oxidoreductase, respiratory chain, transmembrane, transport, formylation, xenon
• Biological source: Thermus thermophilus; More
• Cellular location: Cell membrane; Multi-pass membrane protein: Q5SJ79; Cell membrane; Single-pass membrane protein: Q5SJ80 P82543
• Total number of polymer chains: 3
• Total formula weight: 88427.05

Authors

Luna, V.M.,Chen, Y.,Fee, J.A.,Stout, C.D. (deposition date: 2008-01-07, release date: 2008-05-20, Last modification date: 2023-08-30)

Primary citation

Luna, V.M.,Chen, Y.,Fee, J.A.,Stout, C.D.
Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome ba3 from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases.
Biochemistry, 47:4657-4665, 2008

PubMed Abstract: Cytochrome ba3 is a cytochrome c oxidase from the plasma membrane of Thermus thermophilus and is the preferred terminal enzyme of cellular respiration at low dioxygen tensions. Using cytochrome ba 3 crystals pressurized at varying conditions under Xe or Kr gas, and X-ray data for six crystals, we identify the relative affinities of Xe and Kr atoms for as many as seven distinct binding sites. These sites track a continuous, Y-shaped channel, 18-20 A in length, lined by hydrophobic residues, which leads from the surface of the protein where two entrance holes, representing the top of the Y, connect the bilayer to the a3-CuB center at the base of the Y. Considering the increased affinity of O2 for hydrophobic environments, the hydrophobic nature of the channel, its orientation within the bilayer, its connection to the active site, its uniform diameter, its virtually complete occupation by Xe, and its isomorphous presence in the native enzyme, we infer that the channel is a diffusion pathway for O2 into the dinuclear center of cytochrome ba3. These observations provide a basis for analyzing similar channels in other oxidases of known structure, and these structures are discussed in terms of mechanisms of O2 transport in biological systems, details of CO binding to and egress from the dinuclear center, the bifurcation of the oxygen-in and water-out pathways, and the possible role of the oxygen channel in aerobic thermophily.

PubMed: 18376849
DOI: 10.1021/bi800045y

Experimental method

X-RAY DIFFRACTION (3.37 Å)