IDH1 (isocitrate dehydrogenase (NADP(+)) 1)

Gene

• Entrez ID: 3417
• Gene name: Isocitrate dehydrogenase (NADP(+)) 1
• Gene symbol: IDH1
• Synonyms: HEL-216, HEL-S-26, IDCD, IDH, IDP, IDPC, PICD
• Chromosome: 2
• Chromosome location: 2q34
• Summary: Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. Each NADP(+)-dependent isozyme is a homodimer. The protein encoded by this gene is the NADP(+)-dependent isocitrate dehydrogenase found in the cytoplasm and peroxisomes. It contains the PTS-1 peroxisomal targeting signal sequence. The presence of this enzyme in peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2, 4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. The cytoplasmic enzyme serves a significant role in cytoplasmic NADPH production. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121913499	G>A,C,T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs121913500	C>A,G,T	Likely-pathogenic, not-provided, pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT005125	hsa-miR-30a-5p	pSILAC, Proteomics;Other	18668040
MIRT017645	hsa-miR-335-5p	Microarray	18185580
MIRT036500	hsa-miR-1226-3p	CLASH	23622248
MIRT054822	hsa-miR-30c-5p	qRT-PCR, Western blot	24623846

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000287	Function	Magnesium ion binding	IDA	19935646
GO:0004450	Function	Isocitrate dehydrogenase (NADP+) activity	IBA	21873635
GO:0004450	Function	Isocitrate dehydrogenase (NADP+) activity	IDA	10521434, 19935646, 20171178
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005576	Component	Extracellular region	TAS
GO:0005737	Component	Cytoplasm	IDA
GO:0005739	Component	Mitochondrion	IBA	21873635
GO:0005777	Component	Peroxisome	IBA	21873635
GO:0005777	Component	Peroxisome	IDA	10521434
GO:0005782	Component	Peroxisomal matrix	TAS
GO:0005829	Component	Cytosol	IBA	21873635
GO:0005829	Component	Cytosol	IDA	10521434
GO:0005829	Component	Cytosol	TAS
GO:0006097	Process	Glyoxylate cycle	IEA
GO:0006099	Process	Tricarboxylic acid cycle	IEA
GO:0006102	Process	Isocitrate metabolic process	IBA	21873635
GO:0006102	Process	Isocitrate metabolic process	IDA	10521434, 19935646, 20171178
GO:0006103	Process	2-oxoglutarate metabolic process	IDA	19935646
GO:0006103	Process	2-oxoglutarate metabolic process	TAS
GO:0006625	Process	Protein targeting to peroxisome	TAS
GO:0006739	Process	NADP metabolic process	IBA	21873635
GO:0006740	Process	NADPH regeneration	TAS
GO:0006749	Process	Glutathione metabolic process	IEA
GO:0006979	Process	Response to oxidative stress	IEA
GO:0008585	Process	Female gonad development	IEA
GO:0034774	Component	Secretory granule lumen	TAS
GO:0042802	Function	Identical protein binding	IPI	19935646, 21516116, 26436839
GO:0042803	Function	Protein homodimerization activity	IPI	19935646
GO:0043312	Process	Neutrophil degranulation	TAS
GO:0045296	Function	Cadherin binding	HDA	25468996
GO:0048545	Process	Response to steroid hormone	IEA
GO:0050661	Function	NADP binding	IEA
GO:0051287	Function	NAD binding	IEA
GO:0060696	Process	Regulation of phospholipid catabolic process	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0071071	Process	Regulation of phospholipid biosynthetic process	IEA
GO:1904724	Component	Tertiary granule lumen	TAS
GO:1904813	Component	Ficolin-1-rich granule lumen	TAS

Other IDs

• MIM: 147700
• HGNC: 5382
• e!Ensembl: ENSG00000138413

Protein

• UniProt ID: O75874
• Protein name: Isocitrate dehydrogenase [NADP] cytoplasmic (IDH) (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) (IDP) (NADP(+)-specific ICDH) (Oxalosuccinate decarboxylase)
• PDB: 1T09, 1T0L, 3INM, 3MAP, 3MAR, 3MAS, 4I3K, 4I3L, 4KZO, 4L03, 4L04, 4L06, 4UMX, 4UMY, 4XRX, 4XS3, 5DE1, 5GIR, 5K10, 5K11, 5L57, 5L58, 5LGE, 5SUN, 5SVF, 5TQH, 5YFM, 5YFN, 6ADG, 6B0Z, 6BKX, 6BKY, 6BKZ, 6BL0, 6BL1, 6BL2, 6IO0, 6O2Y, 6O2Z, 6PAY, 6Q6F, 6U4J, 6VEI, 6VG0
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00180	Iso_dh	9 → 401	Isocitrate/isopropylmalate dehydrogenase	Domain

• Sequence:

  MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDA
  AEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRL
  VSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAM
  GMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFE
  AQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDG
  KTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALE
  EVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL

• Sequence length: 414