IDI1_YEAST
ID IDI1_YEAST Reviewed; 288 AA.
AC P15496; D6W3Q1;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 198.
DE RecName: Full=Isopentenyl-diphosphate delta-isomerase {ECO:0000305};
DE EC=5.3.3.2 {ECO:0000269|PubMed:2223785, ECO:0000269|PubMed:2681212, ECO:0000269|PubMed:7908830};
DE AltName: Full=Isopentenyl pyrophosphate isomerase {ECO:0000303|PubMed:2681212};
DE Short=IPP isomerase {ECO:0000303|PubMed:2681212};
GN Name=IDI1 {ECO:0000303|PubMed:2681212}; Synonyms=BOT2;
GN OrderedLocusNames=YPL117C; ORFNames=LPH10C;
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], PROTEIN SEQUENCE OF 2-36, FUNCTION,
RP CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND PATHWAY.
RX PubMed=2681212; DOI=10.1016/s0021-9258(19)47283-9;
RA Anderson M.S., Muehlbacher M., Street I.P., Proffitt J., Poulter C.D.;
RT "Isopentenyl diphosphate:dimethylallyl diphosphate isomerase. An improved
RT purification of the enzyme and isolation of the gene from Saccharomyces
RT cerevisiae.";
RL J. Biol. Chem. 264:19169-19175(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(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 124-154, ACTIVE SITE, FUNCTION, CATALYTIC ACTIVITY, AND
RP ACTIVITY REGULATION.
RX PubMed=2223785; DOI=10.1021/bi00484a023;
RA Street I.P., Poulter C.D.;
RT "Isopentenyldiphosphate:dimethylallyldiphosphate isomerase: construction of
RT a high-level heterologous expression system for the gene from Saccharomyces
RT cerevisiae and identification of an active-site nucleophile.";
RL Biochemistry 29:7531-7538(1990).
RN [5]
RP PROTEIN SEQUENCE OF 196-215, CATALYTIC ACTIVITY, FUNCTION,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, AND MUTAGENESIS OF CYS-138;
RP CYS-139 AND GLU-207.
RX PubMed=7908830; DOI=10.1021/bi00180a014;
RA Street I.P., Coffman H.R., Baker J.A., Poulter C.D.;
RT "Identification of Cys139 and Glu207 as catalytically important groups in
RT the active site of isopentenyl diphosphate:dimethylallyl diphosphate
RT isomerase.";
RL Biochemistry 33:4212-4217(1994).
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 [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-7, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [10]
RP REVIEW ON ERGOSTEROL BIOSYNTHESIS.
RX PubMed=32679672; DOI=10.3390/genes11070795;
RA Jorda T., Puig S.;
RT "Regulation of ergosterol biosynthesis in Saccharomyces cerevisiae.";
RL Genes (Basel) 11:0-0(2020).
CC -!- FUNCTION: Isopentenyl-diphosphate delta-isomerase; part of the second
CC module of ergosterol biosynthesis pathway that includes the middle
CC steps of the pathway (PubMed:2223785, PubMed:2681212, PubMed:7908830).
CC IDI1 catalyzes the 1,3-allylic rearrangement of isopentenyl (IPP) to
CC its highly electrophilic allylic isomer, dimethylallyl diphosphate
CC (DMAPP) (PubMed:2223785, PubMed:2681212, PubMed:7908830). The second
CC module is carried out in the vacuole and involves the formation of
CC farnesyl diphosphate, which is also an important intermediate in the
CC biosynthesis of ubiquinone, dolichol, heme and prenylated proteins.
CC Activity by the mevalonate kinase ERG12 first converts mevalonate into
CC 5-phosphomevalonate. 5-phosphomevalonate is then further converted to
CC 5-diphosphomevalonate by the phosphomevalonate kinase ERG8. The
CC diphosphomevalonate decarboxylase MVD1/ERG19 then produces isopentenyl
CC diphosphate. The isopentenyl-diphosphate delta-isomerase IDI1 then
CC catalyzes the 1,3-allylic rearrangement of the homoallylic substrate
CC isopentenyl (IPP) to its highly electrophilic allylic isomer,
CC dimethylallyl diphosphate (DMAPP). Finally the farnesyl diphosphate
CC synthase ERG20 catalyzes the sequential condensation of isopentenyl
CC pyrophosphate with dimethylallyl pyrophosphate, and then with the
CC resultant geranylpyrophosphate to the ultimate product farnesyl
CC pyrophosphate (PubMed:32679672). {ECO:0000269|PubMed:2223785,
CC ECO:0000269|PubMed:2681212, ECO:0000269|PubMed:7908830,
CC ECO:0000303|PubMed:32679672}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=isopentenyl diphosphate = dimethylallyl diphosphate;
CC Xref=Rhea:RHEA:23284, ChEBI:CHEBI:57623, ChEBI:CHEBI:128769;
CC EC=5.3.3.2; Evidence={ECO:0000269|PubMed:2223785,
CC ECO:0000269|PubMed:2681212, ECO:0000269|PubMed:7908830};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:23285;
CC Evidence={ECO:0000269|PubMed:2223785, ECO:0000269|PubMed:2681212,
CC ECO:0000269|PubMed:7908830};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q46822};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250|UniProtKB:Q46822};
CC -!- ACTIVITY REGULATION: 3,4-epoxy-l-butenyl diphosphate and 3-
CC (fluoromethyl)-3-butenyl diphosphate (FIPP) act as specific active
CC site-directed inhibitors of IP Pisomerase. {ECO:0000269|PubMed:2223785,
CC ECO:0000269|PubMed:2681212}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=43 uM for isopentenyl-diphosphate {ECO:0000269|PubMed:7908830};
CC Vmax=20 umol/min/mg enzyme {ECO:0000269|PubMed:7908830};
CC -!- PATHWAY: Isoprenoid biosynthesis; dimethylallyl diphosphate
CC biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate:
CC step 1/1. {ECO:0000269|PubMed:2223785, ECO:0000269|PubMed:2681212,
CC ECO:0000269|PubMed:7908830}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 25500 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the IPP isomerase type 1 family. {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; J05090; AAA34708.1; -; Genomic_DNA.
DR EMBL; U43503; AAB68245.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11317.1; -; Genomic_DNA.
DR PIR; A34440; A34440.
DR RefSeq; NP_015208.1; NM_001183931.1.
DR AlphaFoldDB; P15496; -.
DR SMR; P15496; -.
DR BioGRID; 36064; 146.
DR IntAct; P15496; 14.
DR MINT; P15496; -.
DR STRING; 4932.YPL117C; -.
DR iPTMnet; P15496; -.
DR MaxQB; P15496; -.
DR PaxDb; P15496; -.
DR PRIDE; P15496; -.
DR EnsemblFungi; YPL117C_mRNA; YPL117C; YPL117C.
DR GeneID; 855986; -.
DR KEGG; sce:YPL117C; -.
DR SGD; S000006038; IDI1.
DR VEuPathDB; FungiDB:YPL117C; -.
DR eggNOG; KOG0142; Eukaryota.
DR GeneTree; ENSGT00390000008527; -.
DR HOGENOM; CLU_060552_0_2_1; -.
DR InParanoid; P15496; -.
DR OMA; DNGLTEH; -.
DR BioCyc; MetaCyc:YPL117C-MON; -.
DR BioCyc; YEAST:YPL117C-MON; -.
DR BRENDA; 5.3.3.2; 984.
DR Reactome; R-SCE-191273; Cholesterol biosynthesis.
DR UniPathway; UPA00059; UER00104.
DR PRO; PR:P15496; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; P15496; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0045337; P:farnesyl diphosphate biosynthetic process; IDA:SGD.
DR GO; GO:0009240; P:isopentenyl diphosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0016126; P:sterol biosynthetic process; IEA:UniProtKB-KW.
DR CDD; cd02885; IPP_Isomerase; 1.
DR InterPro; IPR011876; IsopentenylPP_isomerase_typ1.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR TIGRFAMs; TIGR02150; IPP_isom_1; 1.
DR PROSITE; PS51462; NUDIX; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Direct protein sequencing; Isomerase; Isoprene biosynthesis;
KW Lipid biosynthesis; Lipid metabolism; Magnesium; Metal-binding;
KW Phosphoprotein; Reference proteome; Steroid biosynthesis;
KW Steroid metabolism; Sterol biosynthesis; Sterol metabolism.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2681212"
FT CHAIN 2..288
FT /note="Isopentenyl-diphosphate delta-isomerase"
FT /id="PRO_0000205231"
FT DOMAIN 102..259
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT REGION 33..58
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 39..56
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 139
FT /evidence="ECO:0000269|PubMed:2223785"
FT ACT_SITE 207
FT /evidence="ECO:0000269|PubMed:7908830"
FT BINDING 89
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q13907"
FT BINDING 93
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q46822"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q46822"
FT BINDING 123
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q13907"
FT BINDING 127
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q13907"
FT BINDING 140
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q13907"
FT BINDING 205
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q46822"
FT BINDING 207
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q46822"
FT MOD_RES 7
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MUTAGEN 138
FT /note="C->S,V: 10-fold reduction in activity."
FT /evidence="ECO:0000269|PubMed:7908830"
FT MUTAGEN 139
FT /note="C->A,V: Inactive."
FT /evidence="ECO:0000269|PubMed:7908830"
FT MUTAGEN 139
FT /note="C->S: Reduces activity over 100000-fold."
FT /evidence="ECO:0000269|PubMed:7908830"
FT MUTAGEN 207
FT /note="E->Q,V: Inactive."
FT /evidence="ECO:0000269|PubMed:7908830"
SQ SEQUENCE 288 AA; 33352 MW; 44A373A62EAE1C70 CRC64;
MTADNNSMPH GAVSSYAKLV QNQTPEDILE EFPEIIPLQQ RPNTRSSETS NDESGETCFS
GHDEEQIKLM NENCIVLDWD DNAIGAGTKK VCHLMENIEK GLLHRAFSVF IFNEQGELLL
QQRATEKITF PDLWTNTCCS HPLCIDDELG LKGKLDDKIK GAITAAVRKL DHELGIPEDE
TKTRGKFHFL NRIHYMAPSN EPWGEHEIDY ILFYKINAKE NLTVNPNVNE VRDFKWVSPN
DLKTMFADPS YKFTPWFKII CENYLFNWWE QLDDLSEVEN DRQIHRML
