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isopentenyl-diphosphate Δ-isomerase 1

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Target id: 646

Nomenclature: isopentenyl-diphosphate Δ-isomerase 1

Family: Lanosterol biosynthesis pathway

Contents:

Gene and Protein Information Click here for help
Species TM AA Chromosomal Location Gene Symbol Gene Name Reference
Human - 227 10p15.3 IDI1 isopentenyl-diphosphate delta isomerase 1 3
Mouse - 227 13 A1 Idi1 isopentenyl-diphosphate delta isomerase
Rat - 227 17q12.1 Idi1 isopentenyl-diphosphate delta isomerase 1
Previous and Unofficial Names Click here for help
IPPI1 | methylbutenylpyrophosphate isomerase | IPP isomerase 1 | isopentenyl pyrophosphate isomerase 1
Database Links Click here for help
Alphafold Q13907 (Hs), P58044 (Mm), O35760 (Rn)
BRENDA 5.3.3.2
ChEMBL Target CHEMBL4523132 (Rn)
Ensembl Gene ENSG00000067064 (Hs), ENSMUSG00000058258 (Mm), ENSRNOG00000016690 (Rn)
Entrez Gene 3422 (Hs), 319554 (Mm), 89784 (Rn)
Human Protein Atlas ENSG00000067064 (Hs)
KEGG Enzyme 5.3.3.2
KEGG Gene hsa:3422 (Hs), mmu:319554 (Mm), rno:89784 (Rn)
OMIM 604055 (Hs)
Pharos Q13907 (Hs)
RefSeq Nucleotide NM_004508 (Hs), NM_145360 (Mm), NM_053539 (Rn)
RefSeq Protein NP_004499 (Hs), NP_663335 (Mm), NP_445991 (Rn)
UniProtKB Q13907 (Hs), P58044 (Mm), O35760 (Rn)
Wikipedia IDI1 (Hs)
Selected 3D Structures Click here for help
Image of receptor 3D structure from RCSB PDB
Description:  The crystal structure of human isopentenyl diphophate isomerase
PDB Id:  2ICJ
Resolution:  1.7Å
Species:  Human
References:  6
Image of receptor 3D structure from RCSB PDB
Description:  Human isopentenyl diphophate isomerase complexed with substrate analog
PDB Id:  2ICK
Ligand:  dimethylallyl diphosphate   This ligand is endogenous
Resolution:  1.93Å
Species:  Human
References:  6
Enzyme Reaction Click here for help
EC Number: 5.3.3.2 Isopentenyl diphosphate = dimethylallyl diphosphate
Substrates and Reaction Kinetics Click here for help
Substrate Sp. Property Value Units Standard property Standard value Assay description Assay conditions Comments Reference
isopentenyl diphosphate Substrate is endogenous in the given species Hs Km 3.3x10-5 M pKm 4.5 Recombinant human protein expressed in E coli and purified pH 7, 37°C Km value obtained using the Grafit curve-fitting programme. 10-500 µM IPP; 20mM MgCl2 2
isopentenyl diphosphate Substrate is endogenous in the given species Hs Vmax 4.1 µmol/min/mg Recombinant human protein expressed in E coli and purified. 0.02µg of enzyme used in assay. pH 7, 37°C Vmax value obtained using the Grafit curve-fitting programme. 10-500 µM IPP; 20mM MgCl2 2
Cofactors Click here for help
Cofactor Species Comments Reference
Mg2+ Human Enzyme activity increases with increasing Mg2+ up to 20mM. 2
Mn2+ Human Activity increases up to a concentration of 100 micromolar Mn2+ then sharply decreases. 2,5

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Inhibitors
Key to terms and symbols View all chemical structures Click column headers to sort
Ligand Sp. Action Value Parameter Reference
NE21650 Small molecule or natural product Click here for species-specific activity table Hs Inhibition ~4.2 pIC50 4
⤷ pIC50 ~4.2 (IC50 ~7x10-5 M) [4]
Description: in vitro inhibition assay
Conditions: Recombinant enzyme expressed and partially purified. pH 7.0, 37°C; 10mM MgCl2
Tissue Distribution Comments
Ubiquitously expressed [1].

References

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1. Breitling R, Laubner D, Clizbe D, Adamski J, Krisans SK. (2003) Isopentenyl-diphosphate isomerases in human and mouse: evolutionary analysis of a mammalian gene duplication. J Mol Evol, 57 (3): 282-91. [PMID:14629038]

2. Hahn FM, Xuan JW, Chambers AF, Poulter CD. (1996) Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization. Arch Biochem Biophys, 332 (1): 30-4. [PMID:8806705]

3. Kato T, Emi M, Sato H, Arawaka S, Wada M, Kawanami T, Katagiri T, Tsuburaya K, Toyoshima I, Tanaka F et al.. (2010) Segmental copy-number gain within the region of isopentenyl diphosphate isomerase genes in sporadic amyotrophic lateral sclerosis. Biochem Biophys Res Commun, 402 (2): 438-42. [PMID:20955688]

4. Thompson K, Dunford JE, Ebetino FH, Rogers MJ. (2002) Identification of a bisphosphonate that inhibits isopentenyl diphosphate isomerase and farnesyl diphosphate synthase. Biochem Biophys Res Commun, 290 (2): 869-73. [PMID:11785983]

5. Zhang C, Liu L, Xu H, Wei Z, Wang Y, Lin Y, Gong W. (2007) Crystal structures of human IPP isomerase: new insights into the catalytic mechanism. J Mol Biol, 366 (5): 1437-46. [PMID:17137593]

6. Zheng W, Sun F, Bartlam M, Li X, Li R, Rao Z. (2007) The crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis. J Mol Biol, 366 (5): 1447-58. [PMID:17250851]

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