RCF2_YEAST
ID RCF2_YEAST Reviewed; 224 AA.
AC P53721; D6W1J3;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Respiratory supercomplex factor 2, mitochondrial;
DE AltName: Full=Altered inheritance of mitochondria protein 38;
GN Name=RCF2; Synonyms=AIM38; OrderedLocusNames=YNR018W; ORFNames=N3185;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 76625 / YPH499;
RX PubMed=14576278; DOI=10.1073/pnas.2135385100;
RA Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E.,
RA Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P.,
RA Pfanner N., Meisinger C.;
RT "The proteome of Saccharomyces cerevisiae mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003).
RN [6]
RP DISRUPTION PHENOTYPE.
RX PubMed=19300474; DOI=10.1371/journal.pgen.1000407;
RA Hess D.C., Myers C.L., Huttenhower C., Hibbs M.A., Hayes A.P., Paw J.,
RA Clore J.J., Mendoza R.M., Luis B.S., Nislow C., Giaever G., Costanzo M.,
RA Troyanskaya O.G., Caudy A.A.;
RT "Computationally driven, quantitative experiments discover genes required
RT for mitochondrial biogenesis.";
RL PLoS Genet. 5:E1000407-E1000407(2009).
RN [7]
RP ASSOCIATION WITH THE RESPIRATORY CHAIN COMPLEX IV.
RX PubMed=19750512; DOI=10.1002/pmic.200800951;
RA Helbig A.O., de Groot M.J., van Gestel R.A., Mohammed S., de Hulster E.A.,
RA Luttik M.A., Daran-Lapujade P., Pronk J.T., Heck A.J., Slijper M.;
RT "A three-way proteomics strategy allows differential analysis of yeast
RT mitochondrial membrane protein complexes under anaerobic and aerobic
RT conditions.";
RL Proteomics 9:4787-4798(2009).
RN [8]
RP FUNCTION, AND ASSOCIATION WITH THE RESPIRATORY CHAIN COMPLEX III/COMPLEX IV
RP SUPERCOMPLEX.
RX PubMed=22342701; DOI=10.1016/j.cmet.2012.01.016;
RA Vukotic M., Oeljeklaus S., Wiese S., Vogtle F.N., Meisinger C., Meyer H.E.,
RA Zieseniss A., Katschinski D.M., Jans D.C., Jakobs S., Warscheid B.,
RA Rehling P., Deckers M.;
RT "Rcf1 mediates cytochrome oxidase assembly and respirasome formation,
RT revealing heterogeneity of the enzyme complex.";
RL Cell Metab. 15:336-347(2012).
RN [9]
RP FUNCTION, AND ASSOCIATION WITH THE RESPIRATORY CHAIN COMPLEX III/COMPLEX IV
RP SUPERCOMPLEX.
RX PubMed=22310663; DOI=10.1128/mcb.06369-11;
RA Strogolova V., Furness A., Robb-McGrath M., Garlich J., Stuart R.A.;
RT "Rcf1 and Rcf2, members of the hypoxia-induced gene 1 protein family, are
RT critical components of the mitochondrial cytochrome bc1-cytochrome c
RT oxidase supercomplex.";
RL Mol. Cell. Biol. 32:1363-1373(2012).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [11]
RP FUNCTION.
RX PubMed=30683696; DOI=10.1074/jbc.ra118.006888;
RA Strogolova V., Hoang N.H., Hosler J., Stuart R.A.;
RT "The yeast mitochondrial proteins Rcf1 and Rcf2 support the enzymology of
RT the cytochrome c oxidase complex and generation of the proton motive
RT force.";
RL J. Biol. Chem. 294:4867-4877(2019).
RN [12]
RP FUNCTION.
RX PubMed=31591265; DOI=10.1074/jbc.ra119.010317;
RA Hoang N.H., Strogolova V., Mosley J.J., Stuart R.A., Hosler J.;
RT "Hypoxia-inducible gene domain 1 proteins in yeast mitochondria protect
RT against proton leak through complex IV.";
RL J. Biol. Chem. 294:17669-17677(2019).
RN [13]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=30598554; DOI=10.1038/s41594-018-0172-z;
RA Hartley A.M., Lukoyanova N., Zhang Y., Cabrera-Orefice A., Arnold S.,
RA Meunier B., Pinotsis N., Marechal A.;
RT "Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome
RT bc1.";
RL Nat. Struct. Mol. Biol. 26:78-83(2019).
RN [14]
RP STRUCTURE BY NMR, AND TOPOLOGY.
RX PubMed=29240987; DOI=10.1002/cbic.201700664;
RA Zhou S., Pettersson P., Brzezinski P., Aedelroth P., Maeler L.;
RT "NMR study of Rcf2 reveals an unusual dimeric topology in detergent
RT micelles.";
RL ChemBioChem 19:444-447(2018).
CC -!- FUNCTION: Assembly factor that plays a role in the assembly of the
CC respiratory chain supercomplexes (SCs) composed of ubiquinol-cytochrome
CC c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and
CC cytochrome c oxidase (complex IV, CIV). May be required for late-stage
CC assembly of the COX12 and COX13 subunits (PubMed:22342701,
CC PubMed:22310663). Required for the generation and maintenance of a
CC normal proton motive force (PMF) across the inner mitochondrial
CC membrane (IMM) by preventing proton leakage through an inactive
CC population of CIV that accumulates when RCF1 and/or RCF2 proteins are
CC absent (PubMed:30683696, PubMed:31591265).
CC {ECO:0000269|PubMed:22310663, ECO:0000269|PubMed:22342701,
CC ECO:0000269|PubMed:30683696, ECO:0000269|PubMed:31591265}.
CC -!- SUBUNIT: Associates with a subpopulation of the cytochrome bc1-
CC cytochrome c oxidase supercomplexes (PubMed:19750512, PubMed:22342701,
CC PubMed:22310663). Associates in substoichiometric amounts with complex
CC IV (PubMed:22310663). Interacts with COX3 (PubMed:22310663).
CC {ECO:0000269|PubMed:19750512, ECO:0000269|PubMed:22310663,
CC ECO:0000269|PubMed:22342701}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion membrane {ECO:0000255|PROSITE-
CC ProRule:PRU00836, ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:14576278}; Multi-pass membrane protein
CC {ECO:0000255|PROSITE-ProRule:PRU00836, ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:14576278}.
CC -!- DISRUPTION PHENOTYPE: Increases frequency of mitochondrial genome loss.
CC {ECO:0000269|PubMed:19300474}.
CC -!- MISCELLANEOUS: Present with 12000 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
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DR EMBL; Z71633; CAA96297.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10559.1; -; Genomic_DNA.
DR PIR; S63349; S63349.
DR RefSeq; NP_014415.1; NM_001183195.1.
DR PDB; 6LUL; NMR; -; A/B=1-224.
DR PDB; 6T0B; EM; 2.80 A; m/z=1-224.
DR PDB; 6T15; EM; 3.29 A; m=1-224.
DR PDBsum; 6LUL; -.
DR PDBsum; 6T0B; -.
DR PDBsum; 6T15; -.
DR AlphaFoldDB; P53721; -.
DR SMR; P53721; -.
DR BioGRID; 35843; 144.
DR DIP; DIP-2726N; -.
DR IntAct; P53721; 3.
DR MINT; P53721; -.
DR STRING; 4932.YNR018W; -.
DR TCDB; 8.A.112.2.1; the respiratory supercomplex factor (rcf) family.
DR MaxQB; P53721; -.
DR PaxDb; P53721; -.
DR PRIDE; P53721; -.
DR EnsemblFungi; YNR018W_mRNA; YNR018W; YNR018W.
DR GeneID; 855752; -.
DR KEGG; sce:YNR018W; -.
DR SGD; S000005301; RCF2.
DR VEuPathDB; FungiDB:YNR018W; -.
DR eggNOG; ENOG502QT50; Eukaryota.
DR HOGENOM; CLU_079101_3_0_1; -.
DR InParanoid; P53721; -.
DR OMA; RHEYGII; -.
DR BioCyc; YEAST:G3O-33333-MON; -.
DR PRO; PR:P53721; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P53721; protein.
DR GO; GO:0031305; C:integral component of mitochondrial inner membrane; IDA:SGD.
DR GO; GO:0005746; C:mitochondrial respirasome; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0033617; P:mitochondrial cytochrome c oxidase assembly; IGI:SGD.
DR GO; GO:0010155; P:regulation of proton transport; IMP:SGD.
DR InterPro; IPR007667; Hypoxia_induced_domain.
DR InterPro; IPR040153; Rcf2.
DR PANTHER; PTHR28018; PTHR28018; 1.
DR Pfam; PF04588; HIG_1_N; 1.
DR PROSITE; PS51503; HIG1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Membrane; Mitochondrion; Reference proteome; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..224
FT /note="Respiratory supercomplex factor 2, mitochondrial"
FT /id="PRO_0000215780"
FT TOPO_DOM 1..13
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000250|UniProtKB:Q03713"
FT TRANSMEM 14..38
FT /note="Helical; Name=1"
FT /evidence="ECO:0000269|PubMed:29240987"
FT TOPO_DOM 39..47
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000250|UniProtKB:Q03713"
FT TRANSMEM 48..75
FT /note="Helical; Name=2"
FT /evidence="ECO:0000269|PubMed:29240987"
FT TOPO_DOM 76..103
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000250|UniProtKB:Q03713"
FT TRANSMEM 104..133
FT /note="Helical; Name=3"
FT /evidence="ECO:0000269|PubMed:29240987"
FT TOPO_DOM 134..142
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000250|UniProtKB:Q03713"
FT TRANSMEM 143..173
FT /note="Helical; Name=4"
FT /evidence="ECO:0000269|PubMed:29240987"
FT TOPO_DOM 174..184
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000250|UniProtKB:Q03713"
FT TRANSMEM 185..204
FT /note="Helical; Name=5"
FT /evidence="ECO:0000269|PubMed:29240987"
FT TOPO_DOM 205..224
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000250|UniProtKB:Q03713"
FT DOMAIN 89..180
FT /note="HIG1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00836"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:6LUL"
FT HELIX 17..41
FT /evidence="ECO:0007829|PDB:6LUL"
FT HELIX 48..54
FT /evidence="ECO:0007829|PDB:6LUL"
FT HELIX 56..65
FT /evidence="ECO:0007829|PDB:6LUL"
FT HELIX 67..75
FT /evidence="ECO:0007829|PDB:6LUL"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:6LUL"
FT HELIX 90..99
FT /evidence="ECO:0007829|PDB:6LUL"
FT HELIX 104..107
FT /evidence="ECO:0007829|PDB:6LUL"
FT TURN 109..113
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 119..136
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 143..172
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 175..178
FT /evidence="ECO:0007829|PDB:6T0B"
FT TURN 179..183
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 184..203
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 211..220
FT /evidence="ECO:0007829|PDB:6LUL"
SQ SEQUENCE 224 AA; 25344 MW; FA2C528A008CFE7C CRC64;
MKILTQDEIE AHRSHTLKGG IEGALAGFAI SAIIFKVLPR RYPKFKPSTL TWSIKTALWI
TPPTVLTAIC AEEASNNFDA TMYGSGSSSE DALDEHRRWK SLSTKDKFVE GLSNNKYKII
TGAWAASLYG SWVIVNKDPI MTKAQKIVQA RMYAQFITVG LLLASVGLSM YENKLHPNKQ
KVNEMRRWEN ALRVAEEEER LEKEGRRTGY VSNEERINSK IFKS
