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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: -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).

Miscellaneous

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

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.

Cofactori

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

Pathwayi: dimethylallyl 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)DescriptionActionsGraphical viewLength
Binding sitei89SubstrateBy similarity1
Metal bindingi93MagnesiumBy similarity1
Metal bindingi104MagnesiumBy similarity1
Binding sitei123SubstrateBy similarity1
Binding sitei127SubstrateBy similarity1
Active sitei139By similarity1
Binding sitei140SubstrateBy similarity1
Metal bindingi205MagnesiumBy similarity1
Active sitei207By similarity1
Metal bindingi207MagnesiumBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processIsoprene biosynthesis, Lipid biosynthesis, Lipid metabolism, Steroid biosynthesis, Steroid metabolism, Sterol biosynthesis, Sterol metabolism
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:YPL117C-MONOMER
YEAST:YPL117C-MONOMER
ReactomeiR-SCE-191273 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
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL117C
SGDiS000006038 IDI1

Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi138C → S or V: 10-fold reduction in activity. 1 Publication1
Mutagenesisi139C → A or V: Inactive. 1 Publication1
Mutagenesisi139C → S: Reduces activity over 100000-fold. 1 Publication1
Mutagenesisi207E → Q or V: Inactive. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00002052312 – 288Isopentenyl-diphosphate Delta-isomeraseAdd BLAST287

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei7PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP15496
PaxDbiP15496
PRIDEiP15496

PTM databases

iPTMnetiP15496

Interactioni

Protein-protein interaction databases

BioGridi36064, 144 interactors
IntActiP15496, 18 interactors
MINTiP15496
STRINGi4932.YPL117C

Structurei

3D structure databases

ProteinModelPortaliP15496
SMRiP15496
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini102 – 259Nudix hydrolasePROSITE-ProRule annotationAdd BLAST158

Sequence similaritiesi

Belongs to the IPP isomerase type 1 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000008527
HOGENOMiHOG000274106
InParanoidiP15496
KOiK01823
OMAiLWWDNLH
OrthoDBiEOG092C48JI

Family and domain databases

CDDicd02885 IPP_Isomerase, 1 hit
InterProiView protein in InterPro
IPR011876 IsopentenylPP_isomerase_typ1
IPR015797 NUDIX_hydrolase-like_dom_sf
IPR000086 NUDIX_hydrolase_dom
PANTHERiPTHR10885 PTHR10885, 1 hit
PfamiView protein in Pfam
PF00293 NUDIX, 1 hit
PIRSFiPIRSF018427 Isopntndiph_ism, 1 hit
SUPFAMiSSF55811 SSF55811, 1 hit
TIGRFAMsiTIGR02150 IPP_isom_1, 1 hit
PROSITEiView protein in PROSITE
PS51462 NUDIX, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiIDI1_YEAST
AccessioniPrimary (citable) accession number: P15496
Secondary accession number(s): D6W3Q1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 175 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health