Isopentenyl-diphosphate Delta-isomerase 1

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Reviewed, UniProtKB/Swiss-Prot Q13907 (IDI1_HUMAN)

Last modified June 16, 2009. Version 90. History...

Clusters with 100%, 90%, 50% identity |

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length	227 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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.7
Catalytic activity	Isopentenyl diphosphate = dimethylallyl diphosphate.
Cofactor	Binds 1 magnesium ion per subunit. Ref.7
Pathway	Isoprenoid biosynthesis; dimethylallyl-PP biosynthesis; dimethylallyl-PP from isopentenyl-PP: step 1/1.
Subunit structure	Monomer. Ref.9
Subcellular location	Peroxisome.
Sequence similarities	Belongs to the IPP isomerase type 1 family.

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Ontologies

Keywords
Biological process	Carotenoid biosynthesis Cholesterol biosynthesis Isoprene biosynthesis Lipid synthesis Steroid biosynthesis Sterol biosynthesis
Cellular component	Peroxisome
Ligand	Magnesium Metal-binding
Molecular function	Isomerase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	carotenoid biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW cholesterol biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytosol Ref.7 Inferred from Experiment. Source: Reactome peroxisome Traceable author statement. Source: ProtInc
Molecular function	hydrolase activity Inferred from electronic annotation. Source: InterPro isopentenyl-diphosphate delta-isomerase activity Ref.1 Traceable author statement. Source: ProtInc magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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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

Motif

225 – 227

Microbody targeting signal

Sites

Active site

148

Metal binding

Magnesium

Metal binding

Magnesium

Metal binding

146

Magnesium

Metal binding

148

Magnesium

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Experimental info

Sequence conflict

I → V in BAD96595. Ref.5

Sequence conflict

101

A → T in AAH19227. Ref.6

Sequence conflict

156

R → G in BAD96595. Ref.5

Sequence conflict

173

Y → H in AAH06999. Ref.6

Secondary structure

227

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q13907-1 [UniParc].

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

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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: 8020941] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[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].
[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].
[5]	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]. Tissue: Liver.
[6]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Bone marrow, Skin and Urinary bladder.
[7]	"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: 8806705] [Abstract] Cited for: FUNCTION, COFACTOR.
[8]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[9]	"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: 17250851] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND METAL IONS, SUBUNIT.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

X17025 mRNA. Translation: CAA34890.1. Different initiation.
AF291755 Genomic DNA. Translation: AAK29357.1. Different initiation.
AF271720 mRNA. Translation: AAK49435.1. Different initiation.
AF271724

AF271723 Genomic DNA. Translation: AAK49434.1. Different initiation.
BT006761 mRNA. Translation: AAP35407.1. Different initiation.
AK222875 mRNA. Translation: BAD96595.1. Different initiation.
BC005247 mRNA. Translation: AAH05247.2. Different initiation.
BC006999 mRNA. Translation: AAH06999.2. Different initiation.
BC019227 mRNA. Translation: AAH19227.2. Different initiation.
BC022418 mRNA. Translation: AAH22418.2. Different initiation.
BC025375 mRNA. Translation: AAH25375.2. Different initiation.
BC057827 mRNA. Translation: AAH57827.1. Different initiation.
BC107893 mRNA. Translation: AAI07894.1. Different initiation.

IPI

IPI00220014.

UniGene

Hs.283652
Hs.705849

3D structure databases

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	[»]

ModBase

Search...

Proteomic databases

PRIDE

Q13907.

Genome annotation databases

Ensembl

ENSG00000067064. Homo sapiens. [Contig view]

NMPDR

fig|9606.3.peg.3477.

Organism-specific databases

GeneCards

GC10M001075.

H-InvDB

HIX0008587.

HGNC

HGNC:5387. IDI1.

MIM

604055. gene.

PharmGKB

PA29635.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

Q13907.

Enzyme and pathway databases

BRENDA

5.3.3.2. 247.

Reactome

REACT_602. Lipid and lipoprotein metabolism.

Gene expression databases

ArrayExpress

Q13907.

Bgee

Q13907.

CleanEx

HS_IDI1.

GermOnline

ENSG00000067064. Homo sapiens.

Family and domain databases

InterPro

IPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_core.
[Graphical view]

Gene3D

G3DSA:3.90.79.10. NUDIX_hydrolase. 1 hit.

PANTHER

PTHR10885. IPP_isom_1. 1 hit.

Pfam

PF00293. NUDIX. 1 hit.
[Graphical view]

PIRSF

PIRSF018427. Isopntndiph_ism. 1 hit.

ProDom

PD004109. IPP_isomerase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR02150. IPP_isom_1. 1 hit.

ProtoNet

Search...

Other Resources

SOURCE

Search...

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Entry information

Entry name

IDI1_HUMAN

Accession

Primary (citable) accession number: Q13907
Secondary accession number(s): Q32Q13

Q9BQ74

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 30, 2000
Last modified:	June 16, 2009
This is version 90 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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