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Protein

Isopentenyl-diphosphate Delta-isomerase 1

Gene

Idi1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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 1 (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 sitei36 – 361SubstrateBy similarity
Metal bindingi40 – 401MagnesiumBy similarity
Metal bindingi51 – 511MagnesiumBy similarity
Binding sitei70 – 701SubstrateBy similarity
Binding sitei74 – 741SubstrateBy similarity
Active sitei86 – 861By similarity
Binding sitei87 – 871SubstrateBy similarity
Metal bindingi146 – 1461MagnesiumBy similarity
Active sitei148 – 1481By similarity
Metal bindingi148 – 1481MagnesiumBy similarity

GO - Molecular functioni

  • hydrolase activity Source: InterPro
  • isopentenyl-diphosphate delta-isomerase activity Source: RGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

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

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BRENDAi5.3.3.2. 5301.
UniPathwayiUPA00059; UER00104.

Names & Taxonomyi

Protein namesi
Recommended name:
Isopentenyl-diphosphate Delta-isomerase 1 (EC:5.3.3.2)
Alternative name(s):
Isopentenyl pyrophosphate isomerase 1
Short name:
IPP isomerase 1
Short name:
IPPI1
Gene namesi
Name:Idi1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi621835. Idi1.

Subcellular locationi

GO - Cellular componenti

  • peroxisome Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Peroxisome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 227227Isopentenyl-diphosphate Delta-isomerase 1PRO_0000205227Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei176 – 1761N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiO35760.
PRIDEiO35760.

PTM databases

iPTMnetiO35760.
PhosphoSiteiO35760.

Expressioni

Gene expression databases

BgeeiENSRNOG00000016690.
GenevisibleiO35760. RN.

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000022389.

Structurei

3D structure databases

ProteinModelPortaliO35760.
SMRiO35760. Positions 4-227.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini49 – 199151Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi225 – 2273Microbody targeting signal

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG0142. Eukaryota.
COG1443. LUCA.
HOGENOMiHOG000274106.
HOVERGENiHBG002995.
InParanoidiO35760.
KOiK01823.
OrthoDBiEOG091G0LWP.
PhylomeDBiO35760.
TreeFamiTF300129.

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]
PIRSFiPIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O35760-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEINASNLD EKQVQLLAEM CILIDENDNK IGADTKKNCH LNENIDKGLI
60 70 80 90 100
HRAFSVFLFN TENKLLLQQR SDAKITFPGC FTNSCCSHPL NNPGELEEND
110 120 130 140 150
AMGVKRAAQR RLKAELGIPL EEVDLNEMNY LTRIYYKAQS DGIWGEHEID
160 170 180 190 200
YILFLRKNVT LNPDPNEIKS YCYVSKEELK EILKKEARGE IKLTPWFKII
210 220
ADAFLFKWWD NLNHLSPFVD HEKIHRM
Length:227
Mass (Da):26,396
Last modified:May 15, 2007 - v2
Checksum:i58943AED08D74DB0
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti110 – 1101R → K in AAC53282 (PubMed:9228075).Curated
Sequence conflicti193 – 1931L → F in AAC53282 (PubMed:9228075).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF003835 mRNA. Translation: AAC53282.1.
BC089786 mRNA. Translation: AAH89786.2.
RefSeqiNP_445991.2. NM_053539.2.
UniGeneiRn.10780.

Genome annotation databases

GeneIDi89784.
KEGGirno:89784.
UCSCiRGD:621835. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF003835 mRNA. Translation: AAC53282.1.
BC089786 mRNA. Translation: AAH89786.2.
RefSeqiNP_445991.2. NM_053539.2.
UniGeneiRn.10780.

3D structure databases

ProteinModelPortaliO35760.
SMRiO35760. Positions 4-227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000022389.

PTM databases

iPTMnetiO35760.
PhosphoSiteiO35760.

Proteomic databases

PaxDbiO35760.
PRIDEiO35760.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi89784.
KEGGirno:89784.
UCSCiRGD:621835. rat.

Organism-specific databases

CTDi3422.
RGDi621835. Idi1.

Phylogenomic databases

eggNOGiKOG0142. Eukaryota.
COG1443. LUCA.
HOGENOMiHOG000274106.
HOVERGENiHBG002995.
InParanoidiO35760.
KOiK01823.
OrthoDBiEOG091G0LWP.
PhylomeDBiO35760.
TreeFamiTF300129.

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BRENDAi5.3.3.2. 5301.

Miscellaneous databases

PROiO35760.

Gene expression databases

BgeeiENSRNOG00000016690.
GenevisibleiO35760. RN.

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]
PIRSFiPIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiIDI1_RAT
AccessioniPrimary (citable) accession number: O35760
Secondary accession number(s): Q5FVT3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 15, 2007
Last modified: September 7, 2016
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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.