scholarly journals Structures of bovine cytochrome oxidase reveal proton active transports

2014 ◽  
Vol 70 (a1) ◽  
pp. C1505-C1505
Author(s):  
Naomine Yano ◽  
Kyoko Shinzawa-Itoh ◽  
Atsuhiro Shimada ◽  
Shuhei Takemutra ◽  
Takako Kawahara ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Electron Transfer ◽  
Cytochrome C ◽  
Water Channel ◽  
Proton Pumping ◽  
Hydrogen Bond Network ◽  
O2 Reduction ◽  
Bond Network ◽  
Full Occupancy ◽  
O2 Binding

Bovine cytochrome c oxidase (CcO) pumps four protons in each catalytic cycle through H-pathway including a hydrogen-bond network and a water channel in tandem. Protons, transferred through the water-channel from the negative side of mitochondrial inner membrane into the hydrogen-bond network, are pumped to the positive side of the membrane electrostatically by net positive charges on a heme (heme a) iron created upon electron transfer to the O2 reduction site. For blockage of backward proton leak from the hydrogen-bond network, which determines the proton-pumping direction, the water channel is closed after O2 binding to initiate proton-pump. Thus, four protons must be collected in the hydrogen-bond network before O2 binding. The X-ray structural analyses of the oxidized/reduced CcO at 1.5/1.6 Å resolution reveal a large cluster composed of ~21 water molecules and a Mg2+ site including Glu198 (Subunit II) bridging CuA and Mg2+. The cluster of the oxidized state have 20 water sites with full occupancy and two sites with partial occupies of water, while that of the reduced state have 19 water sites with full occupancy and 3 sites with partial occupancies. The carboxyl group of Glu198 changes its coordination structure to Mg2+ upon the reduction of the active centers. The cluster is tightly sealed sterically against proton exchanges with the cluster outside except for a short hydrogen-bond network connecting the cluster with H-pathway. Five proton-acceptable groups hydrogen-bonded with the cluster suggest sufficient storage capacity for four proton equivalents. The redox-coupled structural changes in the electron transfer pathway from CuA, the initial electron acceptor from cytochrome c, to heme a suggest redox-driven effective proton donations from the cluster to H-pathway, facilitated by Glu198. These results indicate that the cluster is a crucial element of the proton-pumping system of bovine CcO.

scholarly journals X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O2 activation and unidirectional proton-pump mechanisms

2020 ◽  
Vol 295 (17) ◽  
pp. 5818-5833
Author(s):  
Atsuhiro Shimada ◽  
Yuki Etoh ◽  
Rika Kitoh-Fujisawa ◽  
Ai Sasaki ◽  
Kyoko Shinzawa-Itoh ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Resonance Raman Spectroscopy ◽  
Transmembrane Helix ◽  
Water Channel ◽  
Bound State ◽  
Proton Pumping ◽  
Hydrogen Bond Network ◽  
X Ray ◽  
Catalytic Intermediates ◽  
Bond Network

Cytochrome c oxidase (CcO) reduces O2 to water, coupled with a proton-pumping process. The structure of the O2-reduction site of CcO contains two reducing equivalents, Fea32+ and CuB1+, and suggests that a peroxide-bound state (Fea33+–O−–O−–CuB2+) rather than an O2-bound state (Fea32+–O2) is the initial catalytic intermediate. Unexpectedly, however, resonance Raman spectroscopy results have shown that the initial intermediate is Fea32+–O2, whereas Fea33+–O−–O−–CuB2+ is undetectable. Based on X-ray structures of static noncatalytic CcO forms and mutation analyses for bovine CcO, a proton-pumping mechanism has been proposed. It involves a proton-conducting pathway (the H-pathway) comprising a tandem hydrogen-bond network and a water channel located between the N- and P-side surfaces. However, a system for unidirectional proton-transport has not been experimentally identified. Here, an essentially identical X-ray structure for the two catalytic intermediates (P and F) of bovine CcO was determined at 1.8 Å resolution. A 1.70 Å Fe–O distance of the ferryl center could best be described as Fea34+ = O2−, not as Fea34+–OH−. The distance suggests an ∼800-cm−1 Raman stretching band. We found an interstitial water molecule that could trigger a rapid proton-coupled electron transfer from tyrosine-OH to the slowly forming Fea33+–O−–O−–CuB2+ state, preventing its detection, consistent with the unexpected Raman results. The H-pathway structures of both intermediates indicated that during proton-pumping from the hydrogen-bond network to the P-side, a transmembrane helix closes the water channel connecting the N-side with the hydrogen-bond network, facilitating unidirectional proton-pumping during the P-to-F transition.

Reaction mechanism and phospholipid structures of bovine heart cytochrome c oxidase

2005 ◽  
Vol 33 (5) ◽  
pp. 934-937 ◽  
Author(s):  
S. Yoshikawa
Keyword(s):  
Hydrogen Bond ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Hydrogen Bond Network ◽  
X Ray ◽  
Bovine Heart ◽  
O2 Reduction ◽  
Bond Network ◽  
Electron Reduction ◽  
Enzyme Functions

Bovine heart cytochrome c oxidase is a large multi-component membrane protein containing several phospholipids. X-ray structures of this enzyme at high resolution, determined recently, show a trigonal planar structure of CuB site in the O2 reduction site, which could contribute critically to the four-electron reduction of O2 bound at haem a3, and a hydrogen bond network, through which the proton pump is driven by haem a. The possible roles of phospholipids in the enzyme functions are discussed.

scholarly journals Disruption of a hydrogen bond network in human versus spider monkey cytochrome c affects heme crevice stability

2016 ◽  
Vol 158 ◽  
pp. 62-69 ◽  
Author(s):  
Matthew E. Goldes ◽  
Margaret E. Jeakins-Cooley ◽  
Levi J. McClelland ◽  
Tung-Chung Mou ◽  
Bruce E. Bowler
Keyword(s):  
Hydrogen Bond ◽  
Cytochrome C ◽  
Spider Monkey ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals High-resolution crystal structures of the solubilized domain of porcine cytochromeb5

2015 ◽  
Vol 71 (7) ◽  
pp. 1572-1581 ◽  
Author(s):  
Yu Hirano ◽  
Shigenobu Kimura ◽  
Taro Tamada
Keyword(s):  
Hydrogen Bond ◽  
Electron Transfer ◽  
High Resolution ◽  
Crystal Structures ◽  
Axial Ligand ◽  
Amino Acid Residues ◽  
Hydrogen Bond Network ◽  
Porcine Liver ◽  
Crystal Forms ◽  
Bond Network

Mammalian microsomal cytochromeb5has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochromeb5from porcine liver were determined at sub-angstrom resolution (0.76–0.95 Å) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.

Halides of Macrocyclic Silver(II) Complexes: Crystal Structures with Hydrogen Bond Network and Reaction Kinetics of the Decomposition

2021 ◽  
pp. 120431
Author(s):  
Akinori Honda ◽  
Shunta Kakihara ◽  
Shuhei Ichimura ◽  
Kazuaki Tomono ◽  
Mina Matsushita ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Reaction Kinetics ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Kinetics Of
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