8.A.112.  The Respiratory Supercomplex Factor (Rcf) Family

The Saccharomyces cerevisiae respiratory supercomplex factor 1 (Rcf1) protein is located in the mitochondrial inner membrane where it is involved in formation of supercomplexes composed of respiratory complexes III and IV. Zhou et al. 2018 reported the solution structure of Rcf1, which forms a dimer in dodecylphosphocholine (DPC) micelles, where each monomer consists of a bundle of five TMSs and a short flexible soluble helix (SH), although a hydropathy plot shows only two peaks of hydrophobicity. Three TM helices are unusually charged and provide the dimerization interface consisting of 10 putative salt bridges, defining a 'charge zipper' motif. The dimer structure is supported by molecular dynamics (MD) simulations in DPC, although the simulations show a more dynamic dimer interface than suggested by the NMR data. CD and NMR data indicate that Rcf1 undergoes a structural change when reconstituted in liposomes, supported by MD data, suggesting that the dimer structure is unstable in a planar membrane environment, leading to a dynamic monomer-dimer equilibrium. The Rcf1 dimer interacts with cytochrome c, suggesting a role as an electron-transfer bridge between complexes III and IV (Zhou et al. 2018). The N-terminal domain with the two prominent TMSs belongs to the Hypoxia-induced protein conserved region (the Hig-1-N family) while the C-terminal domain is a region of low complexity but seems to be distantly related to a large number of proteins of diverse function. It may be truncated or absent in some homologues. These proteins are found mostly in eukaryotes, but some are from bacteria.

The Saccharomyces cerevisiae mitochondrial respiratory supercomplex factor 2 (Rcf2) plays a role in assembly of supercomplexes composed of cytochrome bc1 (complex III) and cytochrome c oxidase (complex IV). Zhou et al. 2018 expressed the Rcf2 protein in Escherichia coli, refolded it, and reconstituted it into dodecylphosphocholine (DPC) micelles. The structural properties of Rcf2 were studied by solution NMR, and near complete backbone assignment of Rcf2 was achieved. The secondary structure of Rcf2 contains seven helices, of which five are putative transmembrane (TM) helices, including, unexpectedly, a region formed by a charged 20-residue helix at the C terminus. Further studies demonstrated that Rcf2 forms a dimer, and the charged TM helix is involved in this dimer formation. These results hellp provide a basis for understanding the role of this assembly/regulatory factor in supercomplex formation and function (Zhou et al. 2018).



This family belongs to the .

 

References:

Zhou, S., P. Pettersson, J. Huang, J. Sjöholm, D. Sjöstrand, R. Pomès, M. Högbom, P. Brzezinski, L. Mäler, and P. Ädelroth. (2018). Solution NMR structure of yeast Rcf1, a protein involved in respiratory supercomplex formation. Proc. Natl. Acad. Sci. USA 115: 3048-3053.

Examples:

TC#NameOrganismal TypeExample
8.A.112.1.1

The Saccharomyces cerevisiae respiratory supercomplex factor 1 (Rcf1) protein of 159 aas and 2 apparent TMSs is located in the mitochondrial inner membrane where it is involved in formation of supercomplexes composed of respiratory complexes III and IV (Zhou et al. 2018). See family description for more details.

Rcf1 of Saccharomyces cerevisiae

 
8.A.112.1.2

Rcf1 homolog of 213 aas and 2 predicted TMSs.

Rcf1 of Hypocrea virens (Gliocladium virens) (Trichoderma virens)

 
8.A.112.1.3

Rcf1 homologue with 2 predicted TMSs.

Rcf1 of Tremella mesenterica

 
8.A.112.1.4

Rcf1 homologue of 102 aas and 2 predicted TMSs.  The usual C-terminal domain is lacking.

Rcf1 of Drosophila melanogaster (Fruit fly)

 
8.A.112.1.5

HIG1 domain family member 2A, mitochondrial protein of 106 aas and 2 predicted TMSs.

Rcf1 homologue of Homo sapiens

 
8.A.112.1.6

RING-H2 finger protein ATL48 of 349 aas and 3 predicted TMSs. This protein is involved in the pathway protein ubiquitination

Ring-H2 protein of Arabidopsis thaliana (Mouse-ear cress)

 
8.A.112.1.7

Uncharacterized protein of 107 aas and 2 predicted TMSs.

UP of Guillardia theta

 
Examples:

TC#NameOrganismal TypeExample
8.A.112.2.1

The mitochondrial respiratory supercomplex factor 2 (Rcf2) of 224 aas and 4 apparent TMSs in a 2 + 2 TMS apparent arrangement.  According to Zhou et al. 2018, there is a 5th TMS at the C-terminus, but it is strongly hydrophilic.  See family description for the structure and function of Rcf2.

Rcf2 of Saccharomyces cerevisiae

 
8.A.112.2.2

Rcf2 homologue of 257 aas and 4 apparent TMSs in a 2 + 2 TMS arrangement.

Rcf2 of Xylona heveae

 
8.A.112.2.3

Rcf2 homologue of 209 aas and 4 TMSs.

Rcf2 of Mucor ambiguus

 
8.A.112.2.4

Half sized Rcf2 homologue of 98 aas and 2 TMSs, also showing significant sequence similarity to Rcf1 proteins.

Rcf1/2 homolog of Coffea arabica

 
8.A.112.2.5

Uncharacterized protein of 83 aas and 2 TMSs.

UP of Scleroderma citrinum

 
8.A.112.2.6

Putative hypoxia induced protein of 78 aas and 2 TMSs.

Hypoxia induced protein of Rosa chinensis

 
8.A.112.2.7

Uncharacterized protein of 87 aas and 2 TMSs.

UP of Chlorella variabilis (Green alga)

 
Examples:

TC#NameOrganismal TypeExample
8.A.112.3.1

HIG1 domain protein of 104 aas and 2 TMSs.

HIG1 domain protein of Brachionus plicatilis

 
8.A.112.3.2

Uncharacterized protein of 98 aas and 2 TMSs.

UP of Danaus plexippus

 
8.A.112.3.3

HIG1 domain protein of 82 aas and 2 TMSs.

HIG1 protein of Aphis gossypii

 
8.A.112.3.4

HIG1 domain protein of 110 aas and 3 TMSs.

HIG1 protein of Homo sapiens

 
Examples:

TC#NameOrganismal TypeExample
8.A.112.4.1

Uncharacterized protein of 140 aas and possibly 2 TMSs.

UP of Bacillus subtilis