Q13907 (IDI1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:

IDI1

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	227 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Cholesterol biosynthesis Cholesterol metabolism Isoprene biosynthesis Lipid biosynthesis Lipid metabolism Steroid biosynthesis Steroid metabolism Sterol biosynthesis Sterol metabolism
Cellular component	Peroxisome
Coding sequence diversity	Alternative splicing
Ligand	Magnesium Metal-binding
Molecular function	Isomerase
PTM	Acetylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cholesterol 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: Compara
Cellular_component	cytosol Traceable author statement. Source: Reactome mitochondrion Inferred from electronic annotation. Source: Compara peroxisome Inferred from direct assay PubMed 17180682PubMed 17202134. Source: UniProtKB
Molecular_function	hydrolase 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 227

227

Isopentenyl-diphosphate Delta-isomerase 1

PRO_0000205222

Regions

Domain

49 – 199

151

Nudix hydrolase

Motif

225 – 227

3

Microbody targeting signal

Sites

Active site

86

1

Active site

148

1

Metal binding

40

1

Magnesium

Metal binding

51

1

Magnesium

Metal binding

146

1

Magnesium

Metal binding

148

1

Magnesium

Binding site

36

1

Substrate

Binding site

70

1

Substrate

Binding site

74

1

Substrate

Binding site

87

1

Substrate

Amino acid modifications

Modified residue

176

1

N6-acetyllysine Ref.11

Natural variations

Alternative sequence

1

1

M → MWRGLALARAIGCAARGRGQ WAVRAADCAQSGRHPGPAVV CGRRLISVLEQIRHFVMM in isoform 2.

VSP_037889

Experimental info

Sequence conflict

45

1

I → V in BAD96595. Ref.9

Sequence conflict

101

1

A → T in AAH19227. Ref.8

Sequence conflict

156

1

R → G in BAD96595. Ref.9

Sequence conflict

173

1

Y → H in AAH06999. Ref.8

Isoform 2:

Sequence conflict

39

1

V → G in AAI07894. Ref.8

Secondary structure

1

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227

Helix Strand Turn

Details...

Helix

6 – 8

3

Helix

11 – 16

6

Beta strand

20 – 24

5

Beta strand

30 – 35

6

Helix

36 – 39

4

Helix

42 – 45

4

Turn

46 – 48

3

Beta strand

51 – 59

9

Beta strand

65 – 70

6

Beta strand

75 – 77

3

Beta strand

81 – 87

7

Beta strand

90 – 92

3

Helix

93 – 96

4

Helix

99 – 101

3

Helix

102 – 116

15

Helix

120 – 122

3

Helix

125 – 127

3

Beta strand

128 – 139

12

Beta strand

141 – 156

16

Turn

165 – 167

3

Beta strand

168 – 174

7

Helix

176 – 187

12

Helix

195 – 203

9

Helix

205 – 209

5

Turn

210 – 213

4

Helix

216 – 218

3

Beta strand

224 – 226

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 30, 2000. Version 2. Checksum: 1255ACC2C4D1E8D1	FASTA	227	26,319
	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
	Isoform 2 [UniParc]. Checksum: 80478664FEBD5978	FASTA	284	32,485
	10 20 30 40 50 60 MWRGLALARA IGCAARGRGQ WAVRAADCAQ SGRHPGPAVV CGRRLISVLE QIRHFVMMPE 70 80 90 100 110 120 INTNHLDKQQ VQLLAEMCIL IDENDNKIGA ETKKNCHLNE NIEKGLLHRA FSVFLFNTEN 130 140 150 160 170 180 KLLLQQRSDA KITFPGCFTN TCCSHPLSNP AELEESDALG VRRAAQRRLK AELGIPLEEV 190 200 210 220 230 240 PPEEINYLTR IHYKAQSDGI WGEHEIDYIL LVRKNVTLNP DPNEIKSYCY VSKEELKELL 250 260 270 280 KKAASGEIKI TPWFKIIAAT FLFKWWDNLN HLNQFVDHEK IYRM

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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, MASS SPECTROMETRY.
[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 , 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.

IPI

IPI00220014.
IPI00645307.

RefSeq

NP_004499.2. NM_004508.2.

UniGene

Hs.741176.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DHO	X-ray	1.60	A	1-227	[»]
2I6K	X-ray	2.00	A/B	1-227	[»]
2ICJ	X-ray	1.70	A	1-227	[»]
2ICK	X-ray	1.93	A	1-227	[»]

ProteinModelPortal

Q13907.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q13907. 1 interaction.

STRING

9606.ENSP00000370748.

PTM databases

PhosphoSite

Q13907.

Polymorphism databases

DMDM

6225527.

Proteomic databases

PaxDb

Q13907.

PRIDE

Q13907.

Protocols and materials databases

DNASU

3422.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000381344; ENSP00000370748; ENSG00000067064.

GeneID

3422.

KEGG

hsa:3422.

UCSC

uc001ifz.3. human.

Organism-specific databases

CTD

3422.

GeneCards

GC10M001075.

H-InvDB

HIX0008588.

HGNC

HGNC:5387. IDI1.

HPA

HPA039169.

MIM

604055. gene.

neXtProt

NX_Q13907.

PharmGKB

PA29635.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1443.

HOVERGEN

HBG002995.

InParanoid

Q13907.

KO

K01823.

OMA

YILFLQK.

OrthoDB

EOG4PK28T.

Enzyme and pathway databases

BioCyc

MetaCyc:HS00895-MONOMER.

BRENDA

5.3.3.2. 2681.

Reactome

REACT_111217. Metabolism.

SABIO-RK

Q13907.

UniPathway

UPA00059; UER00104.

Gene expression databases

ArrayExpress

Q13907.

Bgee

Q13907.

CleanEx

HS_IDI1.

Genevestigator

Q13907.

GermOnline

ENSG00000067064. Homo sapiens.

Family and domain databases

Gene3D

3.90.79.10. 1 hit.

InterPro

IPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]

PANTHER

PTHR10885. PTHR10885. 1 hit.

Pfam

PF00293. NUDIX. 1 hit.
[Graphical view]

PIRSF

PIRSF018427. Isopntndiph_ism. 1 hit.

SUPFAM

SSF55811. NUDIX_hydrolase. 1 hit.

TIGRFAMs

TIGR02150. IPP_isom_1. 1 hit.

PROSITE

PS51462. NUDIX. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q13907.

GenomeRNAi

3422.

NextBio

13496.

SOURCE

Search...

Entry information

Entry name

IDI1_HUMAN

Accession

Primary (citable) accession number: Q13907
Secondary accession number(s): B4E155 , Q32Q13, Q53GQ6, Q86U81, Q8WUX8, Q96IZ4, Q9BQ74

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 30, 2000
Last modified:	May 1, 2013
This is version 130 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.