ID IDH1_YEAST Reviewed; 360 AA.
AC P28834; D6W1E2;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1993, sequence version 2.
DT 27-MAR-2024, entry version 195.
DE RecName: Full=Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial;
DE EC=1.1.1.41;
DE AltName: Full=Isocitric dehydrogenase;
DE AltName: Full=NAD(+)-specific ICDH;
DE Flags: Precursor;
GN Name=IDH1; OrderedLocusNames=YNL037C; ORFNames=N2690;
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 PROTEIN SEQUENCE OF 49-61; 72-83;
RP 325-333 AND 339-356.
RX PubMed=1644826; DOI=10.1016/s0021-9258(18)42019-4;
RA Cupp J.R., McAlister-Henn L.;
RT "Cloning and characterization of the gene encoding the IDH1 subunit of
RT NAD(+)-dependent isocitrate dehydrogenase from Saccharomyces cerevisiae.";
RL J. Biol. Chem. 267:16417-16423(1992).
RN [2]
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 [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 PROTEIN SEQUENCE OF 12-27.
RC STRAIN=SG7;
RX PubMed=2198251; DOI=10.1128/jb.172.8.4280-4287.1990;
RA Keys D.A., McAlister-Henn L.;
RT "Subunit structure, expression, and function of NAD(H)-specific isocitrate
RT dehydrogenase in Saccharomyces cerevisiae.";
RL J. Bacteriol. 172:4280-4287(1990).
RN [5]
RP RNA-BINDING.
RX PubMed=7505425; DOI=10.1093/nar/21.23.5328;
RA Elzinga S.D.J., Bednarz A.L., van Oosterum K., Dekker P.J.T., Grivell L.A.;
RT "Yeast mitochondrial NAD(+)-dependent isocitrate dehydrogenase is an RNA-
RT binding protein.";
RL Nucleic Acids Res. 21:5328-5331(1993).
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).
CC -!- FUNCTION: Performs an essential role in the oxidative function of the
CC citric acid cycle. Also binds RNA; specifically to the 5'-untranslated
CC leaders of mitochondrial mRNAs.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH;
CC Xref=Rhea:RHEA:23632, ChEBI:CHEBI:15562, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.41;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit. {ECO:0000250};
CC -!- ACTIVITY REGULATION: Allosterically regulated by several compounds
CC including AMP, NAD(+), and citrate.
CC -!- SUBUNIT: Octamer of two non-identical subunits IDH1 and IDH2.
CC -!- INTERACTION:
CC P28834; P28241: IDH2; NbExp=6; IntAct=EBI-8878, EBI-8883;
CC -!- SUBCELLULAR LOCATION: Mitochondrion.
CC -!- MISCELLANEOUS: Present with 10500 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the isocitrate and isopropylmalate
CC dehydrogenases family. {ECO:0000305}.
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DR EMBL; M95203; AAA34711.1; -; Genomic_DNA.
DR EMBL; Z71313; CAA95904.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10508.1; -; Genomic_DNA.
DR PIR; S31264; S31264.
DR RefSeq; NP_014361.1; NM_001182876.1.
DR PDB; 3BLV; X-ray; 3.20 A; A/C/E/G=12-360.
DR PDB; 3BLW; X-ray; 4.30 A; A/C/E/G/I/K/M/O=12-360.
DR PDB; 3BLX; X-ray; 2.70 A; A/C/E/G/I/K/M/O=12-360.
DR PDBsum; 3BLV; -.
DR PDBsum; 3BLW; -.
DR PDBsum; 3BLX; -.
DR AlphaFoldDB; P28834; -.
DR SMR; P28834; -.
DR BioGRID; 35787; 303.
DR ComplexPortal; CPX-558; Mitochondrial isocitrate dehydrogenase complex (NAD+).
DR DIP; DIP-4376N; -.
DR IntAct; P28834; 26.
DR MINT; P28834; -.
DR STRING; 4932.YNL037C; -.
DR MoonProt; P28834; -.
DR GlyGen; P28834; 6 sites, 1 O-linked glycan (6 sites).
DR MaxQB; P28834; -.
DR PaxDb; 4932-YNL037C; -.
DR PeptideAtlas; P28834; -.
DR EnsemblFungi; YNL037C_mRNA; YNL037C; YNL037C.
DR GeneID; 855691; -.
DR KEGG; sce:YNL037C; -.
DR AGR; SGD:S000004982; -.
DR SGD; S000004982; IDH1.
DR VEuPathDB; FungiDB:YNL037C; -.
DR eggNOG; KOG0784; Eukaryota.
DR GeneTree; ENSGT00950000182989; -.
DR HOGENOM; CLU_031953_0_0_1; -.
DR InParanoid; P28834; -.
DR OMA; TCAHKAN; -.
DR OrthoDB; 143577at2759; -.
DR BioCyc; MetaCyc:YNL037C-MONOMER; -.
DR BioCyc; YEAST:YNL037C-MONOMER; -.
DR BRENDA; 1.1.1.41; 984.
DR Reactome; R-SCE-71403; Citric acid cycle (TCA cycle).
DR BioGRID-ORCS; 855691; 4 hits in 10 CRISPR screens.
DR EvolutionaryTrace; P28834; -.
DR PRO; PR:P28834; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P28834; Protein.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0005758; C:mitochondrial intermembrane space; TAS:Reactome.
DR GO; GO:0005962; C:mitochondrial isocitrate dehydrogenase complex (NAD+); IDA:SGD.
DR GO; GO:0005759; C:mitochondrial matrix; IDA:SGD.
DR GO; GO:0042645; C:mitochondrial nucleoid; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:ComplexPortal.
DR GO; GO:0004449; F:isocitrate dehydrogenase (NAD+) activity; IEA:UniProtKB-EC.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006537; P:glutamate biosynthetic process; TAS:SGD.
DR GO; GO:0006102; P:isocitrate metabolic process; IDA:SGD.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IDA:ComplexPortal.
DR Gene3D; 3.40.718.10; Isopropylmalate Dehydrogenase; 1.
DR InterPro; IPR019818; IsoCit/isopropylmalate_DH_CS.
DR InterPro; IPR004434; Isocitrate_DH_NAD.
DR InterPro; IPR024084; IsoPropMal-DH-like_dom.
DR NCBIfam; TIGR00175; mito_nad_idh; 1.
DR PANTHER; PTHR11835; DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE; 1.
DR PANTHER; PTHR11835:SF42; ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL; 1.
DR Pfam; PF00180; Iso_dh; 1.
DR SMART; SM01329; Iso_dh; 1.
DR SUPFAM; SSF53659; Isocitrate/Isopropylmalate dehydrogenase-like; 1.
DR PROSITE; PS00470; IDH_IMDH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; Direct protein sequencing; Magnesium;
KW Manganese; Metal-binding; Mitochondrion; NAD; Oxidoreductase;
KW Reference proteome; RNA-binding; Transit peptide; Tricarboxylic acid cycle.
FT TRANSIT 1..11
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:2198251"
FT CHAIN 12..360
FT /note="Isocitrate dehydrogenase [NAD] subunit 1,
FT mitochondrial"
FT /id="PRO_0000014431"
FT BINDING 109
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 140
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 228
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P50213"
FT BINDING 228
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 194
FT /note="Critical for catalysis"
FT /evidence="ECO:0000250"
FT STRAND 29..37
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 38..53
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 57..62
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 71..84
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 85..91
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 95..99
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 102..110
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 114..122
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 135..141
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 145..148
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 150..153
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 158..166
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 167..183
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 188..193
FT /evidence="ECO:0007829|PDB:3BLX"
FT TURN 195..197
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 201..216
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 220..226
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 227..236
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 242..246
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 248..262
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 269..276
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:3BLX"
FT TURN 283..286
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 289..291
FT /evidence="ECO:0007829|PDB:3BLV"
FT HELIX 300..313
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 317..331
FT /evidence="ECO:0007829|PDB:3BLX"
FT STRAND 332..335
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 338..340
FT /evidence="ECO:0007829|PDB:3BLX"
FT HELIX 346..358
FT /evidence="ECO:0007829|PDB:3BLX"
SQ SEQUENCE 360 AA; 39324 MW; 0932E7B3CD685240 CRC64;
MLNRTIAKRT LATAAQAERT LPKKYGGRFT VTLIPGDGVG KEITDSVRTI FEAENIPIDW
ETINIKQTDH KEGVYEAVES LKRNKIGLKG LWHTPADQTG HGSLNVALRK QLDIYANVAL
FKSLKGVKTR IPDIDLIVIR ENTEGEFSGL EHESVPGVVE SLKVMTRPKT ERIARFAFDF
AKKYNRKSVT AVHKANIMKL GDGLFRNIIT EIGQKEYPDI DVSSIIVDNA SMQAVAKPHQ
FDVLVTPSMY GTILGNIGAA LIGGPGLVAG ANFGRDYAVF EPGSRHVGLD IKGQNVANPT
AMILSSTLML NHLGLNEYAT RISKAVHETI AEGKHTTRDI GGSSSTTDFT NEIINKLSTM
//
