Cytochrome b/b6 profiles

In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (EC 1.10.2.2) - also known as the bc1 complex or ubiquinol-cytochrome c reductase. This complex is the middle component of the mitochondrial respiratory chain, coupling the transfer of electrons from ubihydroquinone to cytochrome c with the generation of a proton gradient across the mitochondrial membrane. Every bc1 complex contains three common subunits with active redox centers (cytochrome b, cytochrome c1, and the "Rieske" [2Fe-2S] protein (ISP) (see <PDOC00177>)). The mitochondrial system contains additional subunits not present in the bacterial complexes. In plant chloroplasts and cyanobacteria, there is a analogous protein of cytochrome b, cytochrome b6, a component of the plastoquinone-plastocyanin reductase (EC 1.10.99.1), also known as the b6f complex.

Cytochrome b/b6 [1,2] is an integral membrane protein of approximately 400 amino acid residues that has 8 transmembrane segments and four horizontal helices on the intermembrane side (see <PDB:1BE3; C>). The two hemes, bL and bH, are in the center of a four αhelical bundle formed by helices 1 to 4 [3].

In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. The sequence of petB is colinear with the N-terminal part of mitochondrial cytochrome b, while petD corresponds to the C-terminal part. Cytochrome b/b6 non-covalently binds two heme groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two heme groups.

Apart from regions around some of the histidine heme ligands, there are a few conserved regions in the sequence of b/b6. The best conserved of these regions includes an invariant P-E-W triplet which lies in the loop that separates the fifth and sixth transmembrane segments. It seems to be important for electron transfer at the ubiquinone redox site - called Qz or Qo (where o stands for outside) - located on the outer side of the membrane.

A schematic representation of the structure of cytochrome b/b6 is shown below.

                   +---Fe-b562----+
                   | +---Fe-b566--|-+
                   | |            | |
        xxxxxxxxxxxHxHxxxxxxxxxxxxHxHxxxxxxxxxxPEWxxxxxxxxxxxxxxxxxx
        <------------------Cytochrome-b---------------------------->
        <----Cytochrome-b6-petB---------><--Cytochrome-b6-petD----->

We developed two profiles for cytochrome b/b6, one that spans the N-terminal region and also recognizes the petB subunit of plant b6 complex; the other profile is directed against the C-terminal region and recognizes also the plant petD subunit.