HIBCH_YEAST
ID HIBCH_YEAST Reviewed; 500 AA.
AC P28817; D6VS24; Q66RH2;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=3-hydroxyisobutyryl-CoA hydrolase, mitochondrial;
DE EC=3.1.2.4;
DE AltName: Full=3-hydroxyisobutyryl-coenzyme A hydrolase;
DE Short=HIB-CoA hydrolase;
DE Short=HIBYL-CoA-H;
DE AltName: Full=Mitochondrial small ribosomal subunit protein mS47 {ECO:0000303|PubMed:28154081};
GN Name=EHD3; Synonyms=MRP5; OrderedLocusNames=YDR036C; ORFNames=YD9673.08C;
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=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(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 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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-265.
RC STRAIN=ATCC 26109 / X2180;
RX PubMed=2903861; DOI=10.1016/s0021-9258(19)81378-9;
RA Mirande M., Waller J.-P.;
RT "The yeast lysyl-tRNA synthetase gene. Evidence for general amino acid
RT control of its expression and domain structure of the encoded protein.";
RL J. Biol. Chem. 263:18443-18451(1988).
RN [5]
RP FUNCTION.
RX PubMed=11378903; DOI=10.1002/yea.726;
RA Wiederkehr A., Meier K.D., Riezman H.;
RT "Identification and characterization of Saccharomyces cerevisiae mutants
RT defective in fluid-phase endocytosis.";
RL Yeast 18:759-773(2001).
RN [6]
RP ENZYME ACTIVITY.
RX PubMed=12697341; DOI=10.1016/s0168-6445(03)00017-2;
RA Hiltunen J.K., Mursula A.M., Rottensteiner H., Wierenga R.K.,
RA Kastaniotis A.J., Gurvitz A.;
RT "The biochemistry of peroxisomal beta-oxidation in the yeast Saccharomyces
RT cerevisiae.";
RL FEMS Microbiol. Rev. 27:35-64(2003).
RN [7]
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 [8]
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 [9]
RP FUNCTION.
RX PubMed=14566057; DOI=10.1073/pnas.2132527100;
RA Samanta M.P., Liang S.;
RT "Predicting protein functions from redundancies in large-scale protein
RT interaction networks.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:12579-12583(2003).
RN [10]
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 [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-326, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 76625 / YPH499;
RX PubMed=17761666; DOI=10.1074/mcp.m700098-mcp200;
RA Reinders J., Wagner K., Zahedi R.P., Stojanovski D., Eyrich B.,
RA van der Laan M., Rehling P., Sickmann A., Pfanner N., Meisinger C.;
RT "Profiling phosphoproteins of yeast mitochondria reveals a role of
RT phosphorylation in assembly of the ATP synthase.";
RL Mol. Cell. Proteomics 6:1896-1906(2007).
RN [12]
RP SUBCELLULAR LOCATION.
RX PubMed=25609543; DOI=10.1038/ncomms7019;
RA Pfeffer S., Woellhaf M.W., Herrmann J.M., Forster F.;
RT "Organization of the mitochondrial translation machinery studied in situ by
RT cryoelectron tomography.";
RL Nat. Commun. 6:6019-6019(2015).
RN [13]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.30 ANGSTROMS), AND SUBUNIT.
RX PubMed=28154081; DOI=10.1126/science.aal2415;
RA Desai N., Brown A., Amunts A., Ramakrishnan V.;
RT "The structure of the yeast mitochondrial ribosome.";
RL Science 355:528-531(2017).
CC -!- FUNCTION: Component of the mitochondrial ribosome (mitoribosome), a
CC dedicated translation machinery responsible for the synthesis of
CC mitochondrial genome-encoded proteins, including at least some of the
CC essential transmembrane subunits of the mitochondrial respiratory
CC chain. The mitoribosomes are attached to the mitochondrial inner
CC membrane and translation products are cotranslationally integrated into
CC the membrane (PubMed:14566057, PubMed:25609543, PubMed:28154081). mS47
CC has enzymatic activity in vitro, and is able to catalyze the specific
CC hydrolysis of 3-hydroxyisobutyryl-CoA (HIBYL-CoA). However, because the
CC turnover rate of mS47/EHD3 is only a fraction of that of the homologous
CC mammalian enzyme, the physiological function of this activity remains
CC unclear (PubMed:12697341). Has an indirect role in endocytic membrane
CC trafficking (PubMed:11378903). {ECO:0000269|PubMed:11378903,
CC ECO:0000269|PubMed:12697341, ECO:0000305|PubMed:14566057,
CC ECO:0000305|PubMed:25609543, ECO:0000305|PubMed:28154081}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-hydroxy-2-methylpropanoyl-CoA + H2O = 3-hydroxy-2-
CC methylpropanoate + CoA + H(+); Xref=Rhea:RHEA:20888,
CC ChEBI:CHEBI:11805, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57287, ChEBI:CHEBI:57340; EC=3.1.2.4;
CC Evidence={ECO:0000269|PubMed:12697341};
CC -!- SUBUNIT: Component of the mitochondrial small ribosomal subunit (mt-
CC SSU). Mature yeast 74S mitochondrial ribosomes consist of a small (37S)
CC and a large (54S) subunit. The 37S small subunit contains a 15S
CC ribosomal RNA (15S mt-rRNA) and 34 different proteins. The 54S large
CC subunit contains a 21S rRNA (21S mt-rRNA) and 46 different proteins.
CC mS47 forms a protuberance of the yeast mitoribosome and retains a
CC solvent-exposed cavity liekly capable of accommodating a substrate, in
CC accordance with it being an active enzyme as well as an integral
CC constituent of the mitoribosome. {ECO:0000269|PubMed:28154081}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:14576278}. Note=Mitoribosomes are tethered to the
CC mitochondrial inner membrane and spatially aligned with the membrane
CC insertion machinery through two distinct membrane contact sites, formed
CC by the 21S rRNA expansion segment 96-ES1 and the inner membrane protein
CC MBA1. {ECO:0000269|PubMed:25609543}.
CC -!- MISCELLANEOUS: Present with 3950 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the enoyl-CoA hydratase/isomerase family.
CC Mitochondrion-specific ribosomal protein mS47 subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; Z68196; CAA92375.1; -; Genomic_DNA.
DR EMBL; Z74332; CAA98862.1; -; Genomic_DNA.
DR EMBL; AY723769; AAU09686.1; -; Genomic_DNA.
DR EMBL; J04186; AAA66915.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11884.1; -; Genomic_DNA.
DR PIR; S61591; S61591.
DR RefSeq; NP_010321.1; NM_001180344.1.
DR PDB; 5MRC; EM; 3.25 A; 88=36-492.
DR PDB; 5MRE; EM; 3.75 A; 88=36-492.
DR PDB; 5MRF; EM; 4.97 A; 88=36-492.
DR PDBsum; 5MRC; -.
DR PDBsum; 5MRE; -.
DR PDBsum; 5MRF; -.
DR AlphaFoldDB; P28817; -.
DR SMR; P28817; -.
DR BioGRID; 32091; 68.
DR ComplexPortal; CPX-1603; 37S mitochondrial small ribosomal subunit.
DR DIP; DIP-6509N; -.
DR IntAct; P28817; 25.
DR MINT; P28817; -.
DR STRING; 4932.YDR036C; -.
DR iPTMnet; P28817; -.
DR MaxQB; P28817; -.
DR PaxDb; P28817; -.
DR PRIDE; P28817; -.
DR EnsemblFungi; YDR036C_mRNA; YDR036C; YDR036C.
DR GeneID; 851606; -.
DR KEGG; sce:YDR036C; -.
DR SGD; S000002443; EHD3.
DR VEuPathDB; FungiDB:YDR036C; -.
DR eggNOG; KOG1684; Eukaryota.
DR GeneTree; ENSGT00890000139491; -.
DR HOGENOM; CLU_009834_22_0_1; -.
DR InParanoid; P28817; -.
DR OMA; GKPYIAF; -.
DR BioCyc; YEAST:G3O-29650-MON; -.
DR Reactome; R-SCE-70895; Branched-chain amino acid catabolism.
DR PRO; PR:P28817; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P28817; protein.
DR GO; GO:0005743; C:mitochondrial inner membrane; IC:ComplexPortal.
DR GO; GO:0005763; C:mitochondrial small ribosomal subunit; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0003860; F:3-hydroxyisobutyryl-CoA hydrolase activity; IDA:SGD.
DR GO; GO:0003735; F:structural constituent of ribosome; IDA:SGD.
DR GO; GO:0032543; P:mitochondrial translation; IC:SGD.
DR GO; GO:0006574; P:valine catabolic process; IBA:GO_Central.
DR InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
DR InterPro; IPR045004; ECH_dom.
DR InterPro; IPR018376; Enoyl-CoA_hyd/isom_CS.
DR InterPro; IPR032259; HIBYL-CoA-H.
DR PANTHER; PTHR43176; PTHR43176; 1.
DR Pfam; PF16113; ECH_2; 1.
DR SUPFAM; SSF52096; SSF52096; 1.
DR PROSITE; PS00166; ENOYL_COA_HYDRATASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Branched-chain amino acid catabolism; Hydrolase;
KW Mitochondrion; Phosphoprotein; Reference proteome; Ribonucleoprotein;
KW Ribosomal protein.
FT CHAIN 1..500
FT /note="3-hydroxyisobutyryl-CoA hydrolase, mitochondrial"
FT /id="PRO_0000109357"
FT BINDING 124
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 149
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 172
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 180
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 326
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17761666"
FT CONFLICT 139
FT /note="V -> A (in Ref. 3; AAU09686)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 500 AA; 56288 MW; 7187506B4F4BCDC6 CRC64;
MLRNTLKCAQ LSSKYGFKTT TRTFMTTQPQ LNVTDAPPVL FTVQDTARVI TLNRPKKLNA
LNAEMSESMF KTLNEYAKSD TTNLVILKSS NRPRSFCAGG DVATVAIFNF NKEFAKSIKF
FTDEYSLNFQ IATYLKPIVT FMDGITMGGG VGLSIHTPFR IATENTKWAM PEMDIGFFPD
VGSTFALPRI VTLANSNSQM ALYLCLTGEV VTGADAYMLG LASHYVSSEN LDALQKRLGE
ISPPFNNDPQ SAYFFGMVNE SIDEFVSPLP KDYVFKYSNE KLNVIEACFN LSKNGTIEDI
MNNLRQYEGS AEGKAFAQEI KTKLLTKSPS SLQIALRLVQ ENSRDHIESA IKRDLYTAAN
MCMNQDSLVE FSEATKHKLI DKQRVPYPWT KKEQLFVSQL TSITSPKPSL PMSLLRNTSN
VTWTQYPYHS KYQLPTEQEI AAYIEKRTND DTGAKVTERE VLNHFANVIP SRRGKLGIQS
LCKIVCERKC EEVNDGLRWK
