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Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

IDI1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

Pathway:idimethylallyl diphosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Isopentenyl-diphosphate Delta-isomerase (IDI1)
This subpathway is part of the pathway dimethylallyl diphosphate biosynthesis, which is itself part of Isoprenoid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate, the pathway dimethylallyl diphosphate biosynthesis and in Isoprenoid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei89 – 891SubstrateBy similarity
Metal bindingi93 – 931MagnesiumBy similarity
Metal bindingi104 – 1041MagnesiumBy similarity
Binding sitei123 – 1231SubstrateBy similarity
Binding sitei127 – 1271SubstrateBy similarity
Active sitei139 – 1391By similarity
Binding sitei140 – 1401SubstrateBy similarity
Metal bindingi205 – 2051MagnesiumBy similarity
Active sitei207 – 2071By similarity
Metal bindingi207 – 2071MagnesiumBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Isoprene biosynthesis, Lipid biosynthesis, Lipid metabolism, Steroid biosynthesis, Steroid metabolism, Sterol biosynthesis, Sterol metabolism

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-654.
YEAST:YPL117C-MONOMER.
ReactomeiREACT_283157. Cholesterol biosynthesis.
UniPathwayiUPA00059; UER00104.

Names & Taxonomyi

Protein namesi
Recommended name:
Isopentenyl-diphosphate Delta-isomerase (EC:5.3.3.2)
Alternative name(s):
Isopentenyl pyrophosphate isomerase
Short name:
IPP isomerase
Gene namesi
Name:IDI1
Synonyms:BOT2
Ordered Locus Names:YPL117C
ORF Names:LPH10C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL117C.
SGDiS000006038. IDI1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi138 – 1381C → S or V: 10-fold reduction in activity. 1 Publication
Mutagenesisi139 – 1391C → A or V: Inactive. 1 Publication
Mutagenesisi139 – 1391C → S: Reduces activity over 100000-fold. 1 Publication
Mutagenesisi207 – 2071E → Q or V: Inactive. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 288287Isopentenyl-diphosphate Delta-isomerasePRO_0000205231Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei7 – 71Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP15496.
PaxDbiP15496.
PeptideAtlasiP15496.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
itself1EBI-8902,EBI-8902
ARO8P530901EBI-8902,EBI-2042933
COX7P101741EBI-8902,EBI-2050505
ESS1P226961EBI-8902,EBI-6679
GLN1P322881EBI-8902,EBI-7665
HEF3P539781EBI-8902,EBI-6345
IPP1P008171EBI-8902,EBI-9338
PRP40P332031EBI-8902,EBI-701
RFT1P382061EBI-8902,EBI-15028
RNR1P215241EBI-8902,EBI-15234
RNR2P099381EBI-8902,EBI-15240
RSC58Q079791EBI-8902,EBI-36549
RSP5P399401EBI-8902,EBI-16219
TAF6P530401EBI-8902,EBI-18876
TFC7Q124151EBI-8902,EBI-33456
USO1P253861EBI-8902,EBI-20157

Protein-protein interaction databases

BioGridi36064. 45 interactions.
IntActiP15496. 14 interactions.
MINTiMINT-642308.

Structurei

3D structure databases

ProteinModelPortaliP15496.
SMRiP15496. Positions 66-287.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini102 – 259158Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the IPP isomerase type 1 family.Curated
Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG1443.
GeneTreeiENSGT00390000008527.
HOGENOMiHOG000274106.
InParanoidiP15496.
KOiK01823.
OMAiICENYLF.
OrthoDBiEOG7Z0K7M.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERiPTHR10885. PTHR10885. 1 hit.
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P15496-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTADNNSMPH GAVSSYAKLV QNQTPEDILE EFPEIIPLQQ RPNTRSSETS
60 70 80 90 100
NDESGETCFS GHDEEQIKLM NENCIVLDWD DNAIGAGTKK VCHLMENIEK
110 120 130 140 150
GLLHRAFSVF IFNEQGELLL QQRATEKITF PDLWTNTCCS HPLCIDDELG
160 170 180 190 200
LKGKLDDKIK GAITAAVRKL DHELGIPEDE TKTRGKFHFL NRIHYMAPSN
210 220 230 240 250
EPWGEHEIDY ILFYKINAKE NLTVNPNVNE VRDFKWVSPN DLKTMFADPS
260 270 280
YKFTPWFKII CENYLFNWWE QLDDLSEVEN DRQIHRML
Length:288
Mass (Da):33,352
Last modified:January 23, 2007 - v2
Checksum:i44A373A62EAE1C70
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05090 Genomic DNA. Translation: AAA34708.1.
U43503 Genomic DNA. Translation: AAB68245.1.
BK006949 Genomic DNA. Translation: DAA11317.1.
PIRiA34440.
RefSeqiNP_015208.1. NM_001183931.1.

Genome annotation databases

EnsemblFungiiYPL117C; YPL117C; YPL117C.
GeneIDi855986.
KEGGisce:YPL117C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05090 Genomic DNA. Translation: AAA34708.1.
U43503 Genomic DNA. Translation: AAB68245.1.
BK006949 Genomic DNA. Translation: DAA11317.1.
PIRiA34440.
RefSeqiNP_015208.1. NM_001183931.1.

3D structure databases

ProteinModelPortaliP15496.
SMRiP15496. Positions 66-287.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36064. 45 interactions.
IntActiP15496. 14 interactions.
MINTiMINT-642308.

Proteomic databases

MaxQBiP15496.
PaxDbiP15496.
PeptideAtlasiP15496.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL117C; YPL117C; YPL117C.
GeneIDi855986.
KEGGisce:YPL117C.

Organism-specific databases

EuPathDBiFungiDB:YPL117C.
SGDiS000006038. IDI1.

Phylogenomic databases

eggNOGiCOG1443.
GeneTreeiENSGT00390000008527.
HOGENOMiHOG000274106.
InParanoidiP15496.
KOiK01823.
OMAiICENYLF.
OrthoDBiEOG7Z0K7M.

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BioCyciMetaCyc:MONOMER-654.
YEAST:YPL117C-MONOMER.
ReactomeiREACT_283157. Cholesterol biosynthesis.

Miscellaneous databases

NextBioi980831.
PROiP15496.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERiPTHR10885. PTHR10885. 1 hit.
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isopentenyl diphosphate:dimethylallyl diphosphate isomerase. An improved purification of the enzyme and isolation of the gene from Saccharomyces cerevisiae."
    Anderson M.S., Muehlbacher M., Street I.P., Proffitt J., Poulter C.D.
    J. Biol. Chem. 264:19169-19175(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-36.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Isopentenyldiphosphate:dimethylallyldiphosphate isomerase: construction of a high-level heterologous expression system for the gene from Saccharomyces cerevisiae and identification of an active-site nucleophile."
    Street I.P., Poulter C.D.
    Biochemistry 29:7531-7538(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 124-154, ACTIVE SITE.
  5. "Identification of Cys139 and Glu207 as catalytically important groups in the active site of isopentenyl diphosphate:dimethylallyl diphosphate isomerase."
    Street I.P., Coffman H.R., Baker J.A., Poulter C.D.
    Biochemistry 33:4212-4217(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 196-215, ACTIVE SITE, MUTAGENESIS OF CYS-138; CYS-139 AND GLU-207.
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-7, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiIDI1_YEAST
AccessioniPrimary (citable) accession number: P15496
Secondary accession number(s): D6W3Q1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: January 23, 2007
Last modified: July 22, 2015
This is version 153 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 25500 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.