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Protein

Isopentenyl-diphosphate Delta-isomerase 1

Gene

IDI1

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+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

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 2 (IDI2), 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)DescriptionActionsGraphical viewLength
Binding sitei36Substrate1 Publication1
Metal bindingi40Magnesium1
Metal bindingi51Magnesium1
Binding sitei70Substrate1 Publication1
Binding sitei74Substrate1 Publication1
Active sitei861
Binding sitei87Substrate1 Publication1
Metal bindingi146Magnesium1
Active sitei1481
Metal bindingi148Magnesium1

GO - Molecular functioni

  • hydrolase activity Source: InterPro
  • isopentenyl-diphosphate delta-isomerase activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • manganese ion binding Source: UniProtKB
  • 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

BioCyciMetaCyc:HS00895-MONOMER.
ZFISH:HS00895-MONOMER.
BRENDAi5.3.3.2. 2681.
ReactomeiR-HSA-191273. Cholesterol biosynthesis.
R-HSA-2426168. Activation of gene expression by SREBF (SREBP).
SABIO-RKQ13907.
UniPathwayiUPA00059; UER00104.

Chemistry databases

SwissLipidsiSLP:000001219. [Q13907-1]

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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:5387. IDI1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • peroxisome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Peroxisome

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000067064.
PharmGKBiPA29635.

Chemistry databases

GuidetoPHARMACOLOGYi646.

Polymorphism and mutation databases

BioMutaiIDI1.
DMDMi6225527.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002052221 – 227Isopentenyl-diphosphate Delta-isomerase 1Add BLAST227

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei176N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ13907.
MaxQBiQ13907.
PaxDbiQ13907.
PeptideAtlasiQ13907.
PRIDEiQ13907.

PTM databases

iPTMnetiQ13907.
PhosphoSitePlusiQ13907.

Expressioni

Gene expression databases

BgeeiENSG00000067064.
CleanExiHS_IDI1.
ExpressionAtlasiQ13907. baseline and differential.
GenevisibleiQ13907. HS.

Organism-specific databases

HPAiHPA039169.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi109648. 3 interactors.
IntActiQ13907. 1 interactor.
MINTiMINT-3028956.
STRINGi9606.ENSP00000370748.

Structurei

Secondary structure

1227
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 8Combined sources3
Helixi11 – 16Combined sources6
Beta strandi20 – 24Combined sources5
Beta strandi30 – 35Combined sources6
Helixi36 – 39Combined sources4
Helixi42 – 45Combined sources4
Turni46 – 48Combined sources3
Beta strandi51 – 59Combined sources9
Beta strandi65 – 70Combined sources6
Beta strandi75 – 77Combined sources3
Beta strandi81 – 87Combined sources7
Beta strandi90 – 92Combined sources3
Helixi93 – 96Combined sources4
Helixi99 – 101Combined sources3
Helixi102 – 116Combined sources15
Helixi120 – 122Combined sources3
Helixi125 – 127Combined sources3
Beta strandi128 – 139Combined sources12
Beta strandi141 – 156Combined sources16
Turni165 – 167Combined sources3
Beta strandi168 – 174Combined sources7
Helixi176 – 187Combined sources12
Helixi195 – 203Combined sources9
Helixi205 – 209Combined sources5
Turni210 – 213Combined sources4
Helixi216 – 218Combined sources3
Beta strandi224 – 226Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DHOX-ray1.60A1-227[»]
2I6KX-ray2.00A/B1-227[»]
2ICJX-ray1.70A1-227[»]
2ICKX-ray1.93A1-227[»]
ProteinModelPortaliQ13907.
SMRiQ13907.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13907.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini49 – 199Nudix hydrolasePROSITE-ProRule annotationAdd BLAST151

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi225 – 227Microbody targeting signal3

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.
GeneTreeiENSGT00390000008527.
HOVERGENiHBG002995.
InParanoidiQ13907.
KOiK01823.
OMAiCHRVHPE.
OrthoDBiEOG091G0LWP.
PhylomeDBiQ13907.
TreeFamiTF300129.

Family and domain databases

CDDicd02885. IPP_Isomerase. 1 hit.
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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q13907-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MPEINTNHLD KQQVQLLAEM CILIDENDNK IGAETKKNCH LNENIEKGLL
60 70 80 90 100
HRAFSVFLFN TENKLLLQQR SDAKITFPGC FTNTCCSHPL SNPAELEESD
110 120 130 140 150
ALGVRRAAQR RLKAELGIPL EEVPPEEINY LTRIHYKAQS DGIWGEHEID
160 170 180 190 200
YILLVRKNVT LNPDPNEIKS YCYVSKEELK ELLKKAASGE IKITPWFKII
210 220
AATFLFKWWD NLNHLNQFVD HEKIYRM
Length:227
Mass (Da):26,319
Last modified:May 30, 2000 - v2
Checksum:i1255ACC2C4D1E8D1
GO
Isoform 2 (identifier: Q13907-2) [UniParc]FASTAAdd to basket

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

Show »
Length:284
Mass (Da):32,485
Checksum:i80478664FEBD5978
GO

Sequence cautioni

The sequence AAH57827 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAK29357 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAK49434 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAK49435 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAP35407 differs from that shown. Reason: Erroneous initiation.Curated
The sequence CAA34890 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti45I → V in BAD96595 (Ref. 9) Curated1
Sequence conflicti101A → T in AAH19227 (PubMed:15489334).Curated1
Sequence conflicti156R → G in BAD96595 (Ref. 9) Curated1
Sequence conflicti173Y → H in AAH06999 (PubMed:15489334).Curated1
Isoform 2 (identifier: Q13907-2)
Sequence conflicti39V → G in AAI07894 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0378891M → MWRGLALARAIGCAARGRGQ WAVRAADCAQSGRHPGPAVV CGRRLISVLEQIRHFVMM in isoform 2. 2 Publications1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS7056.1. [Q13907-2]
RefSeqiNP_001304884.1. NM_001317955.1.
NP_001304885.1. NM_001317956.1.
NP_001304886.1. NM_001317957.1.
NP_004499.2. NM_004508.3. [Q13907-2]
XP_011517759.1. XM_011519457.1.
UniGeneiHs.283652.
Hs.604449.
Hs.661502.

Genome annotation databases

EnsembliENST00000381344; ENSP00000370748; ENSG00000067064. [Q13907-2]
GeneIDi3422.
KEGGihsa:3422.
UCSCiuc001iga.4. human. [Q13907-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS7056.1. [Q13907-2]
RefSeqiNP_001304884.1. NM_001317955.1.
NP_001304885.1. NM_001317956.1.
NP_001304886.1. NM_001317957.1.
NP_004499.2. NM_004508.3. [Q13907-2]
XP_011517759.1. XM_011519457.1.
UniGeneiHs.283652.
Hs.604449.
Hs.661502.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DHOX-ray1.60A1-227[»]
2I6KX-ray2.00A/B1-227[»]
2ICJX-ray1.70A1-227[»]
2ICKX-ray1.93A1-227[»]
ProteinModelPortaliQ13907.
SMRiQ13907.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109648. 3 interactors.
IntActiQ13907. 1 interactor.
MINTiMINT-3028956.
STRINGi9606.ENSP00000370748.

Chemistry databases

GuidetoPHARMACOLOGYi646.
SwissLipidsiSLP:000001219. [Q13907-1]

PTM databases

iPTMnetiQ13907.
PhosphoSitePlusiQ13907.

Polymorphism and mutation databases

BioMutaiIDI1.
DMDMi6225527.

Proteomic databases

EPDiQ13907.
MaxQBiQ13907.
PaxDbiQ13907.
PeptideAtlasiQ13907.
PRIDEiQ13907.

Protocols and materials databases

DNASUi3422.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000381344; ENSP00000370748; ENSG00000067064. [Q13907-2]
GeneIDi3422.
KEGGihsa:3422.
UCSCiuc001iga.4. human. [Q13907-1]

Organism-specific databases

CTDi3422.
GeneCardsiIDI1.
H-InvDBHIX0008588.
HGNCiHGNC:5387. IDI1.
HPAiHPA039169.
MIMi604055. gene.
neXtProtiNX_Q13907.
OpenTargetsiENSG00000067064.
PharmGKBiPA29635.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0142. Eukaryota.
COG1443. LUCA.
GeneTreeiENSGT00390000008527.
HOVERGENiHBG002995.
InParanoidiQ13907.
KOiK01823.
OMAiCHRVHPE.
OrthoDBiEOG091G0LWP.
PhylomeDBiQ13907.
TreeFamiTF300129.

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BioCyciMetaCyc:HS00895-MONOMER.
ZFISH:HS00895-MONOMER.
BRENDAi5.3.3.2. 2681.
ReactomeiR-HSA-191273. Cholesterol biosynthesis.
R-HSA-2426168. Activation of gene expression by SREBF (SREBP).
SABIO-RKQ13907.

Miscellaneous databases

ChiTaRSiIDI1. human.
EvolutionaryTraceiQ13907.
GenomeRNAii3422.
PROiQ13907.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000067064.
CleanExiHS_IDI1.
ExpressionAtlasiQ13907. baseline and differential.
GenevisibleiQ13907. HS.

Family and domain databases

CDDicd02885. IPP_Isomerase. 1 hit.
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_HUMAN
AccessioniPrimary (citable) accession number: Q13907
Secondary accession number(s): B4E155
, Q32Q13, Q53GQ6, Q86U81, Q8WUX8, Q96IZ4, Q9BQ74
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: November 2, 2016
This is version 161 of the entry and version 2 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

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.