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Q13907 (IDI1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:IDI1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length227 AA.
Sequence statusComplete.
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). Ref.10

Catalytic activity

Isopentenyl diphosphate = dimethylallyl diphosphate.

Cofactor

Binds 1 magnesium ion per subunit. Ref.10

Pathway

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

Subunit structure

Monomer. Ref.13

Subcellular location

Peroxisome.

Sequence similarities

Belongs to the IPP isomerase type 1 family.

Contains 1 nudix hydrolase domain.

Sequence caution

The sequence AAH57827.1 differs from that shown. Reason: Erroneous initiation.

The sequence AAK29357.1 differs from that shown. Reason: Erroneous initiation.

The sequence AAK49434.1 differs from that shown. Reason: Erroneous initiation.

The sequence AAK49435.1 differs from that shown. Reason: Erroneous initiation.

The sequence AAP35407.1 differs from that shown. Reason: Erroneous initiation.

The sequence CAA34890.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processCholesterol biosynthesis
Cholesterol metabolism
Isoprene biosynthesis
Lipid biosynthesis
Lipid metabolism
Steroid biosynthesis
Steroid metabolism
Sterol biosynthesis
Sterol metabolism
   Cellular componentPeroxisome
   Coding sequence diversityAlternative splicing
   LigandMagnesium
Metal-binding
   Molecular functionIsomerase
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcholesterol biosynthetic process

Traceable author statement. Source: Reactome

dimethylallyl diphosphate biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

isoprenoid biosynthetic process

Inferred from direct assay Ref.10. Source: UniProtKB

response to stilbenoid

Inferred from electronic annotation. Source: Ensembl

small molecule metabolic process

Traceable author statement. Source: Reactome

   Cellular_componentcytosol

Traceable author statement. Source: Reactome

mitochondrion

Inferred from electronic annotation. Source: Ensembl

peroxisome

Inferred from direct assay PubMed 17180682PubMed 17202134. Source: UniProtKB

   Molecular_functionhydrolase activity

Inferred from electronic annotation. Source: InterPro

isopentenyl-diphosphate delta-isomerase activity

Inferred from direct assay Ref.10. Source: UniProtKB

magnesium ion binding

Inferred from direct assay Ref.13. Source: UniProtKB

manganese ion binding

Inferred from direct assay Ref.13. Source: UniProtKB

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q13907-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q13907-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MWRGLALARAIGCAARGRGQWAVRAADCAQSGRHPGPAVVCGRRLISVLEQIRHFVMM

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 227227Isopentenyl-diphosphate Delta-isomerase 1
PRO_0000205222

Regions

Domain49 – 199151Nudix hydrolase
Motif225 – 2273Microbody targeting signal

Sites

Active site861
Active site1481
Metal binding401Magnesium
Metal binding511Magnesium
Metal binding1461Magnesium
Metal binding1481Magnesium
Binding site361Substrate
Binding site701Substrate
Binding site741Substrate
Binding site871Substrate

Amino acid modifications

Modified residue1761N6-acetyllysine Ref.11

Natural variations

Alternative sequence11M → MWRGLALARAIGCAARGRGQ WAVRAADCAQSGRHPGPAVV CGRRLISVLEQIRHFVMM in isoform 2.
VSP_037889

Experimental info

Sequence conflict451I → V in BAD96595. Ref.9
Sequence conflict1011A → T in AAH19227. Ref.8
Sequence conflict1561R → G in BAD96595. Ref.9
Sequence conflict1731Y → H in AAH06999. Ref.8
Isoform 2:
Sequence conflict391V → G in AAI07894. Ref.8

Secondary structure

................................................ 227
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: 1255ACC2C4D1E8D1

FASTA22726,319
        10         20         30         40         50         60 
MPEINTNHLD KQQVQLLAEM CILIDENDNK IGAETKKNCH LNENIEKGLL HRAFSVFLFN 

        70         80         90        100        110        120 
TENKLLLQQR SDAKITFPGC FTNTCCSHPL SNPAELEESD ALGVRRAAQR RLKAELGIPL 

       130        140        150        160        170        180 
EEVPPEEINY LTRIHYKAQS DGIWGEHEID YILLVRKNVT LNPDPNEIKS YCYVSKEELK 

       190        200        210        220 
ELLKKAASGE IKITPWFKII AATFLFKWWD NLNHLNQFVD HEKIYRM 

« Hide

Isoform 2 [UniParc].

Checksum: 80478664FEBD5978
Show »

FASTA28432,485

References

« Hide 'large scale' references
[1]"A human promyelocyte mRNA transiently induced by TPA is homologous to yeast IPP isomerase."
Xuan J.W., Kowalski J., Chambers A.F., Denhardt D.T.
Genomics 20:129-131(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]"Two genes for isopentenyl diphosphate isomerase in human."
Masuda K., Breitling R., Krisans S.K., Keller B., Moeller G., Adamski J.
Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Characterisation of a human gene for isopentenyl diphosphate dimethylally diphosphate isomerase 1 (IDI1)."
Masuda K., Krisans S.K., Keller B., Moeller G., Adamski J.
Submitted (MAY-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1).
[4]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[5]"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. expand/collapse author list , 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] (ISOFORM 2).
Tissue: Kidney.
[6]"The DNA sequence and comparative analysis of human chromosome 10."
Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. expand/collapse author list , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]"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] (ISOFORM 1), PARTIAL NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Bone marrow, Skin and Urinary bladder.
[9]Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 40-227 (ISOFORM 2).
Tissue: Liver.
[10]"Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization."
Hahn F.M., Xuan J.W., Chambers A.F., Poulter C.D.
Arch. Biochem. Biophys. 332:30-34(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, COFACTOR.
[11]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-176, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"The crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis."
Zheng W., Sun F., Bartlam M., Li X., Li R., Rao Z.
J. Mol. Biol. 366:1447-1458(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND METAL IONS, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X17025 mRNA. Translation: CAA34890.1. Different initiation.
AF291755 Genomic DNA. Translation: AAK29357.1. Different initiation.
AF271720 mRNA. Translation: AAK49435.1. Different initiation.
AF271724 expand/collapse EMBL AC list , AF271721, AF271722, AF271723 Genomic DNA. Translation: AAK49434.1. Different initiation.
BT006761 mRNA. Translation: AAP35407.1. Different initiation.
AK303669 mRNA. Translation: BAG64667.1.
AC022536 Genomic DNA. No translation available.
CH471072 Genomic DNA. Translation: EAW86521.1.
BC005247 mRNA. Translation: AAH05247.2.
BC006999 mRNA. Translation: AAH06999.2.
BC019227 mRNA. Translation: AAH19227.2.
BC022418 mRNA. Translation: AAH22418.2.
BC025375 mRNA. Translation: AAH25375.2.
BC057827 mRNA. Translation: AAH57827.1. Different initiation.
BC107893 mRNA. Translation: AAI07894.1.
AK222875 mRNA. Translation: BAD96595.1.
CCDSCCDS7056.1. [Q13907-2]
RefSeqNP_004499.2. NM_004508.2. [Q13907-2]
XP_005252502.1. XM_005252445.1.
UniGeneHs.283652.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2DHOX-ray1.60A1-227[»]
2I6KX-ray2.00A/B1-227[»]
2ICJX-ray1.70A1-227[»]
2ICKX-ray1.93A1-227[»]
ProteinModelPortalQ13907.
SMRQ13907. Positions 9-227.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid109648. 3 interactions.
IntActQ13907. 1 interaction.
MINTMINT-3028956.
STRING9606.ENSP00000370748.

Chemistry

GuidetoPHARMACOLOGY646.

PTM databases

PhosphoSiteQ13907.

Polymorphism databases

DMDM6225527.

Proteomic databases

MaxQBQ13907.
PaxDbQ13907.
PRIDEQ13907.

Protocols and materials databases

DNASU3422.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000381344; ENSP00000370748; ENSG00000067064. [Q13907-2]
GeneID3422.
KEGGhsa:3422.
UCSCuc001ifz.3. human. [Q13907-2]

Organism-specific databases

CTD3422.
GeneCardsGC10M001075.
H-InvDBHIX0008588.
HGNCHGNC:5387. IDI1.
HPAHPA039169.
MIM604055. gene.
neXtProtNX_Q13907.
PharmGKBPA29635.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1443.
HOVERGENHBG002995.
InParanoidQ13907.
KOK01823.
OMARLMDERC.
OrthoDBEOG7H4DVK.
PhylomeDBQ13907.
TreeFamTF300129.

Enzyme and pathway databases

BioCycMetaCyc:HS00895-MONOMER.
BRENDA5.3.3.2. 2681.
ReactomeREACT_111217. Metabolism.
SABIO-RKQ13907.
UniPathwayUPA00059; UER00104.

Gene expression databases

ArrayExpressQ13907.
BgeeQ13907.
CleanExHS_IDI1.
GenevestigatorQ13907.

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

EvolutionaryTraceQ13907.
GenomeRNAi3422.
NextBio13496.
PROQ13907.
SOURCESearch...

Entry information

Entry nameIDI1_HUMAN
AccessionPrimary (citable) accession number: Q13907
Secondary accession number(s): B4E155 expand/collapse secondary AC list , Q32Q13, Q53GQ6, Q86U81, Q8WUX8, Q96IZ4, Q9BQ74
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: July 9, 2014
This is version 141 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 10

Human chromosome 10: entries, gene names and cross-references to MIM