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PDBsum entry 3bvd

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Oxidoreductase PDB id
3bvd
Jmol
Contents
Protein chains
550 a.a.
166 a.a.
33 a.a.
Ligands
HEM
HAS
CUA
Metals
_XE ×7
_CU

References listed in PDB file
Key reference
Title 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.
Authors V.M.Luna, Y.Chen, J.A.Fee, C.D.Stout.
Ref. Biochemistry, 2008, 47, 4657-4665.
PubMed id 18376849
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.
Secondary reference #1
Title An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from thermus thermophilus.
Authors B.Liu, V.M.Luna, Y.Chen, C.D.Stout, J.A.Fee.
Ref. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2007, 63, 1029-1034.
PubMed id 18084085
Abstract
Secondary reference #2
Title A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from thermus thermophilus.
Authors L.M.Hunsicker-Wang, R.L.Pacoma, Y.Chen, J.A.Fee, C.D.Stout.
Ref. Acta Crystallogr D Biol Crystallogr, 2005, 61, 340-343. [DOI no: 10.1107/S0907444904033906]
PubMed id 15735345
Full text Abstract
Figure 2.
Figure 2 Electron density at the heme a[3] site and for bound glycerol. (a) Heme a[3] site depicting the 2.48 distance between His384 N [146][epsilon] and Fe (black dashed line). Contour levels are 1 [147][sigma] (blue) and 5 [148][sigma] (red) for 2|F[o]| - |F[c]| electron density and 5 [149][sigma] (cyan) for |F[o]| - |F[c]| positive difference density for the bridging O atom. Distances between the bridging O atom and Fe and Cu[B] are 2.44 and 2.07 , respectively. (b) Unbiased 2|F[o]| - |F[c]| electron-density map of the bound glycerol molecule hydrogen bonded to the O2A atom of the propionate group of heme a[3], Tyr136A OH, His283A O, Glu126B OE2 and Gln151B NE2. Contour levels are 1 [150][sigma] (blue) and 2.5 [151][sigma] (purple).
The above figure is reproduced from the cited reference with permission from the IUCr
PROCHECK
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