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Protein

Isopentenyl-diphosphate delta-isomerase 2

Gene

IDI2

Organism
Homo sapiens (Human)
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).1 Publication

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.

Cofactori

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

Pathwayi

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

  1. hydrolase activity Source: InterPro
  2. isopentenyl-diphosphate delta-isomerase activity Source: UniProtKB
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cholesterol biosynthetic process Source: Reactome
  2. dimethylallyl diphosphate biosynthetic process Source: UniProtKB-UniPathway
  3. isopentenyl diphosphate metabolic process Source: MGI
  4. isoprenoid biosynthetic process Source: UniProtKB
  5. small molecule metabolic process Source: Reactome
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

BioCyciMetaCyc:HS07522-MONOMER.
ReactomeiREACT_9405. Cholesterol biosynthesis.
UniPathwayiUPA00059; UER00104.

Names & Taxonomyi

Protein namesi
Recommended name:
Isopentenyl-diphosphate delta-isomerase 2 (EC:5.3.3.2)
Alternative name(s):
Isopentenyl pyrophosphate isomerase 2
Short name:
IPP isomerase 2
Short name:
IPPI2
Gene namesi
Name:IDI2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:23487. IDI2.

Subcellular locationi

  1. Peroxisome 1 Publication

GO - Cellular componenti

  1. cytosol Source: Reactome
  2. peroxisome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Peroxisome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134935136.

Polymorphism and mutation databases

BioMutaiIDI2.
DMDMi20978506.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 227227Isopentenyl-diphosphate delta-isomerase 2PRO_0000205228Add
BLAST

Proteomic databases

PaxDbiQ9BXS1.
PRIDEiQ9BXS1.

PTM databases

PhosphoSiteiQ9BXS1.

Expressioni

Tissue specificityi

Detected in skeletal muscle.1 Publication

Gene expression databases

BgeeiQ9BXS1.
CleanExiHS_IDI2.
GenevestigatoriQ9BXS1.

Organism-specific databases

HPAiHPA041254.

Interactioni

Protein-protein interaction databases

BioGridi124870. 13 interactions.
IntActiQ9BXS1. 1 interaction.
STRINGi9606.ENSP00000277517.

Structurei

Secondary structure

227
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi1 – 44Combined sources
Helixi11 – 166Combined sources
Beta strandi20 – 245Combined sources
Beta strandi30 – 356Combined sources
Helixi36 – 394Combined sources
Helixi42 – 454Combined sources
Turni46 – 483Combined sources
Beta strandi51 – 599Combined sources
Beta strandi65 – 706Combined sources
Beta strandi75 – 773Combined sources
Beta strandi84 – 874Combined sources
Beta strandi90 – 923Combined sources
Helixi93 – 964Combined sources
Helixi99 – 1013Combined sources
Helixi102 – 11615Combined sources
Turni120 – 1223Combined sources
Helixi125 – 1273Combined sources
Beta strandi128 – 15629Combined sources
Turni165 – 1673Combined sources
Beta strandi168 – 1747Combined sources
Helixi176 – 18813Combined sources
Helixi195 – 2039Combined sources
Helixi205 – 2084Combined sources
Helixi209 – 2113Combined sources
Helixi216 – 2183Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PNYX-ray1.81A1-227[»]
SMRiQ9BXS1. Positions 1-227.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9BXS1.

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 signalSequence Analysis

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1443.
GeneTreeiENSGT00390000008527.
HOGENOMiHOG000274106.
HOVERGENiHBG002995.
InParanoidiQ9BXS1.
KOiK01823.
OMAiYILIANT.
OrthoDBiEOG7H4DVK.
PhylomeDBiQ9BXS1.
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.

Q9BXS1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDINLDWVD RRQLQRLEEM LIVVDENDKV IGADTKRNCH LNENIEKGLL
60 70 80 90 100
HRAFSVVLFN TKNRILIQQR SDTKVTFPGY FTDSCSSHPL YNPAELEEKD
110 120 130 140 150
AIGVRRAAQR RLQAELGIPG EQISPEDIVF MTIYHHKAKS DRIWGEHEIC
160 170 180 190 200
YLLLVRKNVT LNPDPSETKS ILYLSQEELW ELLEREARGE VKVTPWLRTI
210 220
AERFLYRWWP HLDDVTPFVE LHKIHRV
Length:227
Mass (Da):26,753
Last modified:June 1, 2001 - v1
Checksum:i2FD79B076D94A7D0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF291755 Genomic DNA. Translation: AAK29358.1.
AF271729
, AF271726, AF271727, AF271728 Genomic DNA. Translation: AAK49436.1.
AF271725 mRNA. Translation: AAK49437.1.
AK056950 mRNA. Translation: BAB71322.1.
BC017778 mRNA. Translation: AAH17778.1.
CCDSiCCDS7055.1.
RefSeqiNP_150286.1. NM_033261.2.
UniGeneiHs.591325.
Hs.9270.

Genome annotation databases

EnsembliENST00000277517; ENSP00000277517; ENSG00000148377.
GeneIDi91734.
KEGGihsa:91734.
UCSCiuc001ifv.1. human.

Polymorphism and mutation databases

BioMutaiIDI2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF291755 Genomic DNA. Translation: AAK29358.1.
AF271729
, AF271726, AF271727, AF271728 Genomic DNA. Translation: AAK49436.1.
AF271725 mRNA. Translation: AAK49437.1.
AK056950 mRNA. Translation: BAB71322.1.
BC017778 mRNA. Translation: AAH17778.1.
CCDSiCCDS7055.1.
RefSeqiNP_150286.1. NM_033261.2.
UniGeneiHs.591325.
Hs.9270.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PNYX-ray1.81A1-227[»]
SMRiQ9BXS1. Positions 1-227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124870. 13 interactions.
IntActiQ9BXS1. 1 interaction.
STRINGi9606.ENSP00000277517.

PTM databases

PhosphoSiteiQ9BXS1.

Polymorphism and mutation databases

BioMutaiIDI2.
DMDMi20978506.

Proteomic databases

PaxDbiQ9BXS1.
PRIDEiQ9BXS1.

Protocols and materials databases

DNASUi91734.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000277517; ENSP00000277517; ENSG00000148377.
GeneIDi91734.
KEGGihsa:91734.
UCSCiuc001ifv.1. human.

Organism-specific databases

CTDi91734.
GeneCardsiGC10M001064.
H-InvDBHIX0127248.
HGNCiHGNC:23487. IDI2.
HPAiHPA041254.
MIMi615389. gene.
neXtProtiNX_Q9BXS1.
PharmGKBiPA134935136.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1443.
GeneTreeiENSGT00390000008527.
HOGENOMiHOG000274106.
HOVERGENiHBG002995.
InParanoidiQ9BXS1.
KOiK01823.
OMAiYILIANT.
OrthoDBiEOG7H4DVK.
PhylomeDBiQ9BXS1.
TreeFamiTF300129.

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BioCyciMetaCyc:HS07522-MONOMER.
ReactomeiREACT_9405. Cholesterol biosynthesis.

Miscellaneous databases

EvolutionaryTraceiQ9BXS1.
GenomeRNAii91734.
NextBioi77415.
PROiQ9BXS1.
SOURCEiSearch...

Gene expression databases

BgeeiQ9BXS1.
CleanExiHS_IDI2.
GenevestigatoriQ9BXS1.

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...

Publicationsi

« Hide 'large scale' publications
  1. "IDI2, a second isopentenyl diphosphate isomerase in mammals."
    Clizbe D.B., Owens M.L., Masuda K.R., Shackelford J.E., Krisans S.K.
    J. Biol. Chem. 282:6668-6676(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Skeletal muscle.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Skeletal muscle.

Entry informationi

Entry nameiIDI2_HUMAN
AccessioniPrimary (citable) accession number: Q9BXS1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2002
Last sequence update: June 1, 2001
Last modified: April 29, 2015
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. SIMILARITY comments
    Index of protein domains and families

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.