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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: Ubiquitin Ligase (UL) Superfamily .

References associated with 8.A.112 family:

Liu, Y., N. Soetandyo, J.G. Lee, L. Liu, Y. Xu, W.M. Clemons, Jr, and Y. Ye. (2014). USP13 antagonizes gp78 to maintain functionality of a chaperone in ER-associated degradation. Elife 3: e01369. 24424410
Shimizu, K., M. Tani, H. Watanabe, Y. Nagamachi, Y. Niinaka, T. Shiroishi, S. Ohwada, A. Raz, and J. Yokota. (1999). The autocrine motility factor receptor gene encodes a novel type of seven transmembrane protein. FEBS Lett. 456: 295-300. 10456327
Wang, Y.J., Y. Bian, J. Luo, M. Lu, Y. Xiong, S.Y. Guo, H.Y. Yin, X. Lin, Q. Li, C.C.Y. Chang, T.Y. Chang, B.L. Li, and B.L. Song. (2017). Cholesterol and fatty acids regulate cysteine ubiquitylation of ACAT2 through competitive oxidation. Nat. Cell Biol. 19: 808-819. 28604676
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. 29507228
Zhou, S., P. Pettersson, J. Huang, P. Brzezinski, R. Pomès, L. Mäler, and P. Ädelroth. (2021). NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2. Structure 29: 275-283.e4. 32905793