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P15496 (IDI1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 145. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Isopentenyl-diphosphate Delta-isomerase

EC=5.3.3.2
Alternative name(s):
Isopentenyl pyrophosphate isomerase
Short name=IPP isomerase
Gene names
Name:IDI1
Synonyms:BOT2
Ordered Locus Names:YPL117C
ORF Names:LPH10C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length288 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

Isopentenyl diphosphate = dimethylallyl diphosphate.

Cofactor

Binds 1 magnesium ion per subunit By similarity.

Pathway

Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1.

Subcellular location

Cytoplasm.

Miscellaneous

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

Sequence similarities

Belongs to the IPP isomerase type 1 family.

Contains 1 nudix hydrolase domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1
Chain2 – 288287Isopentenyl-diphosphate Delta-isomerase
PRO_0000205231

Regions

Domain102 – 259158Nudix hydrolase

Sites

Active site1391 By similarity
Active site2071 By similarity
Metal binding931Magnesium By similarity
Metal binding1041Magnesium By similarity
Metal binding2051Magnesium By similarity
Metal binding2071Magnesium By similarity
Binding site891Substrate By similarity
Binding site1231Substrate By similarity
Binding site1271Substrate By similarity
Binding site1401Substrate By similarity

Amino acid modifications

Modified residue71Phosphoserine Ref.8

Experimental info

Mutagenesis1381C → S or V: 10-fold reduction in activity. Ref.5
Mutagenesis1391C → A or V: Inactive. Ref.5
Mutagenesis1391C → S: Reduces activity over 100000-fold. Ref.5
Mutagenesis2071E → Q or V: Inactive. Ref.5

Sequences

Sequence LengthMass (Da)Tools
P15496 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 44A373A62EAE1C70

FASTA28833,352
        10         20         30         40         50         60 
MTADNNSMPH GAVSSYAKLV QNQTPEDILE EFPEIIPLQQ RPNTRSSETS NDESGETCFS 

        70         80         90        100        110        120 
GHDEEQIKLM NENCIVLDWD DNAIGAGTKK VCHLMENIEK GLLHRAFSVF IFNEQGELLL 

       130        140        150        160        170        180 
QQRATEKITF PDLWTNTCCS HPLCIDDELG LKGKLDDKIK GAITAAVRKL DHELGIPEDE 

       190        200        210        220        230        240 
TKTRGKFHFL NRIHYMAPSN EPWGEHEIDY ILFYKINAKE NLTVNPNVNE VRDFKWVSPN 

       250        260        270        280 
DLKTMFADPS YKFTPWFKII CENYLFNWWE QLDDLSEVEN DRQIHRML 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J05090 Genomic DNA. Translation: AAA34708.1.
U43503 Genomic DNA. Translation: AAB68245.1.
BK006949 Genomic DNA. Translation: DAA11317.1.
PIRA34440.
RefSeqNP_015208.1. NM_001183931.1.

3D structure databases

ProteinModelPortalP15496.
SMRP15496. Positions 66-287.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36064. 45 interactions.
IntActP15496. 14 interactions.
MINTMINT-642308.
STRING4932.YPL117C.

Proteomic databases

MaxQBP15496.
PaxDbP15496.
PeptideAtlasP15496.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYPL117C; YPL117C; YPL117C.
GeneID855986.
KEGGsce:YPL117C.

Organism-specific databases

SGDS000006038. IDI1.

Phylogenomic databases

eggNOGCOG1443.
GeneTreeENSGT00390000008527.
HOGENOMHOG000274106.
KOK01823.
OMAELLWANT.
OrthoDBEOG7Z0K7M.

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-654.
YEAST:YPL117C-MONOMER.
UniPathwayUPA00059; UER00104.

Gene expression databases

GenevestigatorP15496.

Family and domain databases

Gene3D3.90.79.10. 1 hit.
InterProIPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERPTHR10885. PTHR10885. 1 hit.
PfamPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFPIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMSSF55811. SSF55811. 1 hit.
TIGRFAMsTIGR02150. IPP_isom_1. 1 hit.
PROSITEPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio980831.
PROP15496.

Entry information

Entry nameIDI1_YEAST
AccessionPrimary (citable) accession number: P15496
Secondary accession number(s): D6W3Q1
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 145 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XVI

Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways