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   27-MAR-2024, entry version 195.
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; 49.
DR   DIP; DIP-4314N; -.
DR   IntAct; P40037; 2.
DR   MINT; P40037; -.
DR   STRING; 4932.YER057C; -.
DR   iPTMnet; P40037; -.
DR   MaxQB; P40037; -.
DR   PaxDb; 4932-YER057C; -.
DR   PeptideAtlas; P40037; -.
DR   TopDownProteomics; P40037; -.
DR   EnsemblFungi; YER057C_mRNA; YER057C; YER057C.
DR   GeneID; 856785; -.
DR   KEGG; sce:YER057C; -.
DR   AGR; SGD:S000000859; -.
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; PAKFSHG; -.
DR   OrthoDB; 1935965at2759; -.
DR   BioCyc; YEAST:G3O-30234-MONOMER; -.
DR   BioGRID-ORCS; 856785; 0 hits in 10 CRISPR screens.
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   CDD; cd00448; YjgF_YER057c_UK114_family; 1.
DR   Gene3D; 3.30.1330.40; RutC-like; 1.
DR   InterPro; IPR006056; RidA.
DR   InterPro; IPR019897; RidA_CS.
DR   InterPro; IPR035959; RutC-like_sf.
DR   InterPro; IPR006175; YjgF/YER057c/UK114.
DR   NCBIfam; TIGR00004; Rid family detoxifying hydrolase; 1.
DR   PANTHER; PTHR11803; 2-IMINOBUTANOATE/2-IMINOPROPANOATE DEAMINASE RIDA; 1.
DR   PANTHER; PTHR11803:SF39; 2-IMINOBUTANOATE_2-IMINOPROPANOATE DEAMINASE; 1.
DR   Pfam; PF01042; Ribonuc_L-PSP; 1.
DR   SUPFAM; SSF55298; YjgF-like; 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
//