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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

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

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: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

GO - Cellular componenti

Complete GO annotation...

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.
PRIDEiP15496.

PTM databases

iPTMnetiP15496.

Interactioni

Protein-protein interaction databases

BioGridi36064. 46 interactors.
IntActiP15496. 14 interactors.
MINTiMINT-642308.

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
Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000008527.
HOGENOMiHOG000274106.
InParanoidiP15496.
KOiK01823.
OMAiQVPFEDF.
OrthoDBiEOG092C48JI.

Family and domain databases

CDDicd02885. IPP_Isomerase. 1 hit.
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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36064. 46 interactors.
IntActiP15496. 14 interactors.
MINTiMINT-642308.

PTM databases

iPTMnetiP15496.

Proteomic databases

MaxQBiP15496.
PRIDEiP15496.

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

GeneTreeiENSGT00390000008527.
HOGENOMiHOG000274106.
InParanoidiP15496.
KOiK01823.
OMAiQVPFEDF.
OrthoDBiEOG092C48JI.

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BioCyciMetaCyc:YPL117C-MONOMER.
YEAST:YPL117C-MONOMER.
ReactomeiR-SCE-191273. Cholesterol biosynthesis.

Miscellaneous databases

PROiP15496.

Family and domain databases

CDDicd02885. IPP_Isomerase. 1 hit.
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...

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: November 2, 2016
This is version 163 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

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 one 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.