Complex III of Electron Transport Chain: Difference between revisions

Each cytochrome b contains<scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_b/5'> two hemes</scene> (displayed as spacefill and colored cpk). Identify each of the hemes by toggling off the spin and hovering the curser over an atom of the heme.  Hem 501 and Hem 502 are in one cytochrome b, and Hem 521 and Hem 522 are in the other one.  The two hemes in each cytochrome b are in different environments and therefore have different properties, e.g. reduction potential. Hemes 501 & 521 have a lower potential than the other two and are called b_L for low potential, and the other two are called b_H for high potential. Each of the cytochrome b's have two substrate binding sites, Q_P and Q_N. Q_P is adjacent to the b_L heme and binds [http://en.wikipedia.org/wiki/Ubiquinol ubiquinol] or, <scene name='Complex_III_of_Electron_Transport_Chain/Stigmatellin/1'>as in this case</scene>, the inhibitor <font color='red'>stigmatellin</font><ref name=1KYOmodified>This structure and the next several are generated by a modification of 1KYO.pdb. The Jmol command 'write file' was used to make a PDB file that contains only the 6 active subunits and cytochrome c (chains c,d,e,n,o,p,w) and the cofactors of those peptides. Since 1KYO.pdb contains stigmatellin bound at the Q_P sites, stigmatellin will be used to represent ubiquinol at Q_P in the modified pdb file.  </ref>. The other site, Q_N, is located adjacent to the b_H heme and binds [[Coenzyme_Q10|ubiquinone]], and since it is empty in the PDB file, it is shown as <scene name='Complex_III_of_Electron_Transport_Chain/Surface_antimycin/1'>a surface with pockets</scene>.  In this view you are looking into the lit pocket in which the ubiquinone binds. You can rotate the structure and observe the ubiquinone binding pocket in the other subunit.<br>

<applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1'  /> At the start of the cycle the Q_P site of cytochrome b is empty and the Fe/S center of the Rieske protein is in the 'Int position'. (<scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1'>Reset initial scene.</scene>) With the binding of <scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_cycle/2'>ubiquinol</scene>, UQH₂, to the Q_P site (black arrow) of cytochrome b the Rieske protein moves to the 'cyto b position' by flexing at the hinge region and rotating the Fe/S head so that the His which is bound to the Fe/S also binds to <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle/1'>ubiquinol</scene> (<font color=red>stigmatellin</font> in this model)<ref name=1KYOmodified/>.  Binding of the His to UQH₂ reduces its pK, and the UQH₂ loses a proton to become [http://en.wikipedia.org/wiki/Ubiquinol UQH^{<big> -</big>}].  The position of Q_P in the complex is such that the proton which is lost <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_arrow/1'>diffuses to the intermembrane space</scene>. After UQH₂ loses the proton and becomes UQH^-, it passes an electron through the His to the Fe⁺³ reducing it to Fe⁺².  With the loss of the electron the UQH^{<big> -</big>} becomes UQH<big>^•</big>, a [http://en.wikipedia.org/wiki/Ubiquinol semiquinone], which loses a proton and becomes UQ^{<big> • -</big>}, the conjugate base of the semiquinone.  The proton diffuses to the intermembrane space, as the first one did.  (The fate of the semiquinone can be traced starting with the next paragraph.) After Fe in the Fe/S center is reduced by the UQH^{<big> -</big>}, the Rieske head rotates & the Fe/S moves to cytochrome c1, <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_move_c1/1'>the "c1" position</scene>, so that the second His bound to Fe/S binds to the heme of cytochrome c1. When the His contacts the heme of cytochrome c1 an electron is rapidly passed from the Fe/S through the His to the Fe of the cytochrome c1 heme, and since it is now in the oxidized form, the Rieske protein returns to the "Int" position. The cytochrome c1 heme is now reduced, and when <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_2_cycle/1'>cytochrome c binds</scene> to it the electron is passed from the c1 heme to the c heme (black arrow). The cytochrome c then releases from the membrane and diffuses through the intermembrane space to Complex IV.