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Protein

Isopentenyl-diphosphate Delta-isomerase 1

Gene

IDI1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processCholesterol biosynthesis, Cholesterol metabolism, Isoprene biosynthesis, Lipid biosynthesis, Lipid metabolism, Steroid biosynthesis, Steroid metabolism, Sterol biosynthesis, Sterol metabolism
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:HS00895-MONOMER
BRENDAi5.3.3.2 2681
ReactomeiR-HSA-191273 Cholesterol biosynthesis
R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
SABIO-RKiQ13907
UniPathwayi
UPA00059;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

EuPathDBiHostDB:ENSG00000067064.10
HGNCiHGNC:5387 IDI1
MIMi604055 gene
neXtProtiNX_Q13907

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Peroxisome

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000067064
PharmGKBiPA29635

Chemistry databases

DrugBankiDB01785 Dimethylallyl Diphosphate
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
ProteomicsDBi59723
59724 [Q13907-2]

PTM databases

iPTMnetiQ13907
PhosphoSitePlusiQ13907

Expressioni

Gene expression databases

BgeeiENSG00000067064 Expressed in 231 organ(s), highest expression level in testis
CleanExiHS_IDI1
ExpressionAtlasiQ13907 baseline and differential
GenevisibleiQ13907 HS

Organism-specific databases

HPAiHPA039169

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi109648, 4 interactors
IntActiQ13907, 5 interactors
STRINGi9606.ENSP00000370748

Structurei

Secondary structure

1227
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Phylogenomic databases

eggNOGiKOG0142 Eukaryota
COG1443 LUCA
GeneTreeiENSGT00390000008527
HOVERGENiHBG002995
InParanoidiQ13907
KOiK01823
OMAiLRLCPWF
OrthoDBiEOG091G0LWP
PhylomeDBiQ13907
TreeFamiTF300129

Family and domain databases

CDDicd02885 IPP_Isomerase, 1 hit
InterProiView protein in InterPro
IPR011876 IsopentenylPP_isomerase_typ1
IPR015797 NUDIX_hydrolase-like_dom_sf
IPR000086 NUDIX_hydrolase_dom
PANTHERiPTHR10885 PTHR10885, 1 hit
PfamiView protein in Pfam
PF00293 NUDIX, 1 hit
PIRSFiPIRSF018427 Isopntndiph_ism, 1 hit
SUPFAMiSSF55811 SSF55811, 1 hit
TIGRFAMsiTIGR02150 IPP_isom_1, 1 hit
PROSITEiView protein in PROSITE
PS51462 NUDIX, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

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

This entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
C9JKM8C9JKM8_HUMAN
Isopentenyl-diphosphate Delta-isome...
IDI1
122Annotation score:
C9JD53C9JD53_HUMAN
Isopentenyl-diphosphate Delta-isome...
IDI1
120Annotation score:

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]
ENST00000429642; ENSP00000401879; ENSG00000067064 [Q13907-1]
GeneIDi3422
KEGGihsa:3422
UCSCiuc001iga.4 human [Q13907-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

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, 4 interactors
IntActiQ13907, 5 interactors
STRINGi9606.ENSP00000370748

Chemistry databases

DrugBankiDB01785 Dimethylallyl Diphosphate
GuidetoPHARMACOLOGYi646
SwissLipidsiSLP:000001219 [Q13907-1]

PTM databases

iPTMnetiQ13907
PhosphoSitePlusiQ13907

Polymorphism and mutation databases

BioMutaiIDI1
DMDMi6225527

Proteomic databases

EPDiQ13907
MaxQBiQ13907
PaxDbiQ13907
PeptideAtlasiQ13907
PRIDEiQ13907
ProteomicsDBi59723
59724 [Q13907-2]

Protocols and materials databases

DNASUi3422
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000381344; ENSP00000370748; ENSG00000067064 [Q13907-2]
ENST00000429642; ENSP00000401879; ENSG00000067064 [Q13907-1]
GeneIDi3422
KEGGihsa:3422
UCSCiuc001iga.4 human [Q13907-1]

Organism-specific databases

CTDi3422
EuPathDBiHostDB:ENSG00000067064.10
GeneCardsiIDI1
H-InvDBiHIX0008588
HGNCiHGNC:5387 IDI1
HPAiHPA039169
MIMi604055 gene
neXtProtiNX_Q13907
OpenTargetsiENSG00000067064
PharmGKBiPA29635
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0142 Eukaryota
COG1443 LUCA
GeneTreeiENSGT00390000008527
HOVERGENiHBG002995
InParanoidiQ13907
KOiK01823
OMAiLRLCPWF
OrthoDBiEOG091G0LWP
PhylomeDBiQ13907
TreeFamiTF300129

Enzyme and pathway databases

UniPathwayi
UPA00059;UER00104

BioCyciMetaCyc:HS00895-MONOMER
BRENDAi5.3.3.2 2681
ReactomeiR-HSA-191273 Cholesterol biosynthesis
R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
SABIO-RKiQ13907

Miscellaneous databases

ChiTaRSiIDI1 human
EvolutionaryTraceiQ13907
GenomeRNAii3422
PROiPR:Q13907
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000067064 Expressed in 231 organ(s), highest expression level in testis
CleanExiHS_IDI1
ExpressionAtlasiQ13907 baseline and differential
GenevisibleiQ13907 HS

Family and domain databases

CDDicd02885 IPP_Isomerase, 1 hit
InterProiView protein in InterPro
IPR011876 IsopentenylPP_isomerase_typ1
IPR015797 NUDIX_hydrolase-like_dom_sf
IPR000086 NUDIX_hydrolase_dom
PANTHERiPTHR10885 PTHR10885, 1 hit
PfamiView protein in Pfam
PF00293 NUDIX, 1 hit
PIRSFiPIRSF018427 Isopntndiph_ism, 1 hit
SUPFAMiSSF55811 SSF55811, 1 hit
TIGRFAMsiTIGR02150 IPP_isom_1, 1 hit
PROSITEiView protein in PROSITE
PS51462 NUDIX, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiIDI1_HUMAN
AccessioniPrimary (citable) accession number: Q13907
Secondary accession number(s): B4E155
, Q32Q13, Q53GQ6, Q86U81, Q8WUX8, Q96IZ4, Q9BQ74
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: November 7, 2018
This is version 177 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
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