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3bvd

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3bvd, resolution 3.37Å ()
Ligands: , , , ,
Gene: cbaA (Thermus thermophilus), cbaB, ctaC (Thermus thermophilus), cbaD (Thermus thermophilus)
Activity: Cytochrome-c oxidase, with EC number 1.9.3.1
Related: 2qpd


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Contents

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

Publication Abstract from PubMed

Cytochrome ba 3 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 a 3-Cu B center at the base of the Y. Considering the increased affinity of O 2 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 O 2 into the dinuclear center of cytochrome ba 3. 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 O 2 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.

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(,)., Luna VM, Chen Y, Fee JA, Stout CD, Biochemistry. 2008 Apr 22;47(16):4657-65. Epub 2008 Apr 1. PMID:18376849

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3bvd is a 3 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA.

See Also

Reference

  • Luna VM, Chen Y, Fee JA, Stout CD. 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. 2008 Apr 22;47(16):4657-65. Epub 2008 Apr 1. PMID:18376849 doi:10.1021/bi800045y
  • Liu B, Luna VM, Chen Y, Stout CD, Fee JA. An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Dec 1;63(Pt, 12):1029-34. Epub 2007 Nov 21. PMID:18084085 doi:10.1107/S1744309107054176
  • Hunsicker-Wang LM, Pacoma RL, Chen Y, Fee JA, Stout CD. A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):340-3. Epub 2005, Feb 24. PMID:15735345 doi:10.1107/S0907444904033906

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