HMF1_YEAST
ID HMF1_YEAST Reviewed; 129 AA.
AC P40037; D3DLW1;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 189.
DE RecName: Full=Protein HMF1;
DE AltName: Full=High dosage growth inhibitor;
DE AltName: Full=Homologous mitochondrial matrix factor 1;
GN Name=HMF1; Synonyms=HIG1; OrderedLocusNames=YER057C;
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 [GENOMIC DNA], AND SUBCELLULAR LOCATION.
RX PubMed=11442631; DOI=10.1046/j.1365-2443.2001.00443.x;
RA Kim J.-M., Yoshikawa H., Shirahige K.;
RT "A member of the YER057c/yjgf/Uk114 family links isoleucine biosynthesis
RT and intact mitochondria maintenance in Saccharomyces cerevisiae.";
RL Genes Cells 6:507-517(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP SUBCELLULAR LOCATION.
RX PubMed=11003673; DOI=10.1128/mcb.20.20.7784-7797.2000;
RA Oxelmark E., Marchini A., Malanchi I., Magherini F., Jaquet L.,
RA Hajibagheri M.A., Blight K.J., Jauniaux J.-C., Tommasino M.;
RT "Mmf1p, a novel yeast mitochondrial protein conserved throughout evolution
RT and involved in maintenance of the mitochondrial genome.";
RL Mol. Cell. Biol. 20:7784-7797(2000).
RN [6]
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 [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=22984289; DOI=10.1074/mcp.m112.021105;
RA Voegtle F.N., Burkhart J.M., Rao S., Gerbeth C., Hinrichs J.,
RA Martinou J.C., Chacinska A., Sickmann A., Zahedi R.P., Meisinger C.;
RT "Intermembrane space proteome of yeast mitochondria.";
RL Mol. Cell. Proteomics 11:1840-1852(2012).
RN [8]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-52, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22106047; DOI=10.1002/pmic.201100166;
RA Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL Proteomics 12:236-240(2012).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
RX PubMed=12112709; DOI=10.1002/prot.10151;
RA Deaconescu A.M., Roll-Mecak A., Bonanno J.B., Gerchman S.E., Kycia H.,
RA Studier F.W., Burley S.K.;
RT "X-ray structure of Saccharomyces cerevisiae homologous mitochondrial
RT matrix factor 1 (Hmf1).";
RL Proteins 48:431-436(2002).
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Mitochondrion intermembrane
CC space {ECO:0000269|PubMed:22984289}.
CC -!- MISCELLANEOUS: Present with 672 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RutC family. {ECO:0000305}.
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DR EMBL; AB050475; BAB20815.1; -; Genomic_DNA.
DR EMBL; U18813; AAB64593.1; -; Genomic_DNA.
DR EMBL; AY558456; AAS56782.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07715.1; -; Genomic_DNA.
DR PIR; S50560; S50560.
DR RefSeq; NP_010978.3; NM_001178948.3.
DR PDB; 1JD1; X-ray; 1.70 A; A/B/C/D/E/F=1-129.
DR PDBsum; 1JD1; -.
DR AlphaFoldDB; P40037; -.
DR SMR; P40037; -.
DR BioGRID; 36798; 42.
DR DIP; DIP-4314N; -.
DR IntAct; P40037; 2.
DR MINT; P40037; -.
DR STRING; 4932.YER057C; -.
DR iPTMnet; P40037; -.
DR MaxQB; P40037; -.
DR PaxDb; P40037; -.
DR PRIDE; P40037; -.
DR TopDownProteomics; P40037; -.
DR EnsemblFungi; YER057C_mRNA; YER057C; YER057C.
DR GeneID; 856785; -.
DR KEGG; sce:YER057C; -.
DR SGD; S000000859; HMF1.
DR VEuPathDB; FungiDB:YER057C; -.
DR eggNOG; KOG2317; Eukaryota.
DR GeneTree; ENSGT00420000029792; -.
DR HOGENOM; CLU_100715_7_2_1; -.
DR InParanoid; P40037; -.
DR OMA; GSYFKEP; -.
DR BioCyc; YEAST:G3O-30234-MON; -.
DR EvolutionaryTrace; P40037; -.
DR PRO; PR:P40037; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40037; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0019239; F:deaminase activity; IBA:GO_Central.
DR GO; GO:1901565; P:organonitrogen compound catabolic process; IBA:GO_Central.
DR Gene3D; 3.30.1330.40; -; 1.
DR InterPro; IPR006056; RidA.
DR InterPro; IPR019897; RidA_CS.
DR InterPro; IPR035959; RutC-like_sf.
DR InterPro; IPR006175; YjgF/YER057c/UK114.
DR PANTHER; PTHR11803; PTHR11803; 1.
DR Pfam; PF01042; Ribonuc_L-PSP; 1.
DR SUPFAM; SSF55298; SSF55298; 1.
DR TIGRFAMs; TIGR00004; TIGR00004; 1.
DR PROSITE; PS01094; UPF0076; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Isopeptide bond; Mitochondrion; Nucleus;
KW Reference proteome; Ubl conjugation.
FT CHAIN 1..129
FT /note="Protein HMF1"
FT /id="PRO_0000170312"
FT CROSSLNK 52
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:1JD1"
FT STRAND 17..19
FT /evidence="ECO:0007829|PDB:1JD1"
FT STRAND 22..26
FT /evidence="ECO:0007829|PDB:1JD1"
FT STRAND 29..35
FT /evidence="ECO:0007829|PDB:1JD1"
FT HELIX 49..66
FT /evidence="ECO:0007829|PDB:1JD1"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:1JD1"
FT STRAND 74..82
FT /evidence="ECO:0007829|PDB:1JD1"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:1JD1"
FT HELIX 87..97
FT /evidence="ECO:0007829|PDB:1JD1"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:1JD1"
FT STRAND 104..109
FT /evidence="ECO:0007829|PDB:1JD1"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:1JD1"
FT STRAND 118..126
FT /evidence="ECO:0007829|PDB:1JD1"
SQ SEQUENCE 129 AA; 13906 MW; D1D252BBA47F81E8 CRC64;
MVTTLTPVIC ESAPAAAASY SHAMKVNNLI FLSGQIPVTP DNKLVEGSIA DKAEQVIQNI
KNVLEASNSS LDRVVKVNIF LADINHFAEF NSVYAKYFNT HKPARSCVAV AALPLGVDME
MEAIAAERD
