IDH3A

IDH3A
Identifiers
AliasesIDH3A, isocitrate dehydrogenase 3 (NAD(+)) alpha
External IDsMGI: 1915084 HomoloGene: 4037 GeneCards: IDH3A
Gene location (Human)
Chr.Chromosome 15 (human)[1]
Band15q25.1Start78,131,498 bp[1]
End78,171,949 bp[1]
RNA expression pattern


More reference expression data
Orthologs
SpeciesHumanMouse
Entrez

3419

67834

Ensembl

ENSG00000166411

ENSMUSG00000032279

UniProt

P50213

Q9D6R2

RefSeq (mRNA)

NM_005530

NM_029573

RefSeq (protein)

NP_005521

NP_083849

Location (UCSC)Chr 15: 78.13 – 78.17 MbChr 9: 54.59 – 54.6 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (IDH3α) is an enzyme that in humans is encoded by the IDH3A gene.[5][6]

Isocitrate dehydrogenases (IDHs) 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. NAD(+)-dependent isocitrate dehydrogenases catalyze the allosterically regulated rate-limiting step of the tricarboxylic acid cycle. Each isozyme is a heterotetramer that is composed of two alpha subunits, one beta subunit, and one gamma subunit. The protein encoded by this gene is the alpha subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. [provided by RefSeq, Jul 2008][6]

Structure

IDH3 is one of three isocitrate dehydrogenase isozymes, the other two being IDH1 and IDH2, and encoded by one of five isocitrate dehydrogenase genes, which are IDH1, IDH2, IDH3A, IDH3B, and IDH3G.[7] The genes IDH3A, IDH3B, and IDH3G encode subunits of IDH3, which is a heterotetramer composed of two 37-kDa α subunits (IDH3α), one 39-kDa β subunit (IDH3β), and one 39-kDa γ subunit (IDH3γ), each with distinct isoelectric points.[8][9][10] Alignment of their amino acid sequences reveals ~40% identity between IDH3α and IDH3β, ~42% identity between IDH3α and IDH3γ, and an even closer identity of 53% between IDH3β and IDH3γ, for an overall 34% identity and 23% similarity across all three subunit types.[9][10][11][12] Notably, Arg88 in IDH3α is essential for IDH3 catalytic activity, whereas the equivalent Arg99 in IDH3β and Arg97 in IDH3γ are largely involved in the enzyme’s allosteric regulation by ADP and NAD.[11] Thus, it is possible that these subunits arose from gene duplication of a common ancestral gene, and the original catalytic Arg residue were adapted to allosteric functions in the β- and γ-subunits.[9][11] Likewise, Asp181 in IDH3α is essential for catalysis, while the equivalent Asp192 in IDH3β and Asp190 in IDH3γ enhance NAD- and Mn2+-binding.[9] Since the oxidative decarboxylation catalyzed by IDH3 requires binding of NAD, Mn2+, and the substrate isocitrate, all three subunits participate in the catalytic reaction.[10][11] Moreover, studies of the enzyme in pig heart reveal that the αβ and αγ dimers constitute two binding sites for each of its ligands, including isocitrate, Mn2+, and NAD, in one IDH3 tetramer.[9][10]

Function

As an isocitrate dehydrogenase, IDH3 catalyzes the reversible oxidative decarboxylation of isocitrate to yield α-ketoglutarate (α-KG) and CO2 as part of the TCA cycle in glucose metabolism.[5][8][9][10][11] This step also allows for the concomitant reduction of NAD+ to NADH, which is then used to generate ATP through the electron transport chain. Notably, IDH3 relies on NAD+ as its electron acceptor, as opposed to NADP+ like IDH1 and IDH2.[8][9] IDH3 activity is regulated by the energy needs of the cell: when the cell requires energy, IDH3 is activated by ADP; and when energy is no longer required, IDH3 is inhibited by ATP and NADH.[9][10] This allosteric regulation allows IDH3 to function as a rate-limiting step in the TCA cycle.[5][13] Within cells, IDH3 and its subunits have been observed to localize to the mitochondria.[5][9][10]

Clinical Significance

IDH3α expression has been linked to cancer, with high basal expression in multiple cancer cell lines and increased expression indicative of poorer prognosis in cancer patients. IDH3α is proposed to promote tumor growth as a regulator of α-KG, which subsequently regulates HIF-1. HIF-1 is largely known for shifting glucose metabolism from oxidative phosphorylation to aerobic glycolysis in cancer cells (the Warburg effect). Moreover, IDH3α activity leads to angiogenesis and metabolic reprogramming to provide the necessary nutrients for continuous cell growth. Meanwhile, silencing IDH3α is observed to obstruct tumor growth. Thus, IDH3α may prove to be a promising therapeutic target in treating cancer.[8]

IDH3α is also implicated in psychiatric disorders. In particular, IDH3α expression in the cerebellum is observed to be significantly lower for bipolar disorder, major depressive disorder, and schizophrenia. The abnormal IDH3α levels may disrupt mitochondrial function and contribute to the pathogenesis of these disorders.[13]

See also

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000166411 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000032279 - Ensembl, May 2017
  3. ↑ "Human PubMed Reference:".
  4. ↑ "Mouse PubMed Reference:".
  5. 1 2 3 4 Huh TL, Kim YO, Oh IU, Song BJ, Inazawa J (May 1997). "Assignment of the human mitochondrial NAD+ -specific isocitrate dehydrogenase alpha subunit (IDH3A) gene to 15q25.1→q25.2by in situ hybridization". Genomics. 32 (2): 295–6. doi:10.1006/geno.1996.0120. PMID 8833160.
  6. 1 2 "Entrez Gene: IDH3A isocitrate dehydrogenase 3 (NAD+) alpha".
  7. ↑ Dimitrov L, Hong CS, Yang C, Zhuang Z, Heiss JD (2015). "New developments in the pathogenesis and therapeutic targeting of the IDH1 mutation in glioma". International Journal of Medical Sciences. 12 (3): 201–13. doi:10.7150/ijms.11047. PMC 4323358. PMID 25678837.
  8. 1 2 3 4 Zeng, L; Morinibu, A; Kobayashi, M; Zhu, Y; Wang, X; Goto, Y; Yeom, CJ; Zhao, T; Hirota, K; Shinomiya, K; Itasaka, S; Yoshimura, M; Guo, G; Hammond, EM; Hiraoka, M; Harada, H (3 September 2015). "Aberrant IDH3α expression promotes malignant tumor growth by inducing HIF-1-mediated metabolic reprogramming and angiogenesis". Oncogene. 34 (36): 4758–66. doi:10.1038/onc.2014.411. PMID 25531325.
  9. 1 2 3 4 5 6 7 8 9 Bzymek, KP; Colman, RF (8 May 2007). "Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase". Biochemistry. 46 (18): 5391–7. doi:10.1021/bi700061t. PMID 17432878.
  10. 1 2 3 4 5 6 7 Soundar, S; O'hagan, M; Fomulu, KS; Colman, RF (28 July 2006). "Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase". The Journal of Biological Chemistry. 281 (30): 21073–81. doi:10.1074/jbc.m602956200. PMID 16737955.
  11. 1 2 3 4 5 Soundar, S; Park, JH; Huh, TL; Colman, RF (26 December 2003). "Evaluation by mutagenesis of the importance of 3 arginines in alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase". The Journal of Biological Chemistry. 278 (52): 52146–53. doi:10.1074/jbc.m306178200. PMID 14555658.
  12. ↑ Dange, M; Colman, RF (2 July 2010). "Each conserved active site tyr in the three subunits of human isocitrate dehydrogenase has a different function". The Journal of Biological Chemistry. 285 (27): 20520–5. doi:10.1074/jbc.m110.115386. PMC 2898308. PMID 20435888.
  13. 1 2 Yoshimi, N; Futamura, T; Bergen, SE; Iwayama, Y; Ishima, T; Sellgren, C; Ekman, CJ; Jakobsson, J; Pålsson, E; Kakumoto, K; Ohgi, Y; Yoshikawa, T; Landén, M; Hashimoto, K (19 January 2016). "Cerebrospinal fluid metabolomics identifies a key role of isocitrate dehydrogenase in bipolar disorder: evidence in support of mitochondrial dysfunction hypothesis". Molecular Psychiatry. doi:10.1038/mp.2015.217. PMID 26782057.

Further reading

  • Anderson NL, Anderson NG (2003). "The human plasma proteome: history, character, and diagnostic prospects". Mol. Cell. Proteomics. 1 (11): 845–67. doi:10.1074/mcp.R200007-MCP200. PMID 12488461.
  • Kim YO, Oh IU, Park HS, et al. (1995). "Characterization of a cDNA clone for human NAD(+)-specific isocitrate dehydrogenase alpha-subunit and structural comparison with its isoenzymes from different species". Biochem. J. 308 (Pt 1): 63–8. PMC 1136843. PMID 7755589.
  • Maruyama K, Sugano S (1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1–2): 171–4. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
  • Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, et al. (1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1–2): 149–56. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
  • Kim YO, Koh HJ, Kim SH, et al. (2000). "Identification and functional characterization of a novel, tissue-specific NAD(+)-dependent isocitrate dehydrogenase beta subunit isoform". J. Biol. Chem. 274 (52): 36866–75. doi:10.1074/jbc.274.52.36866. PMID 10601238.
  • Weiss C, Zeng Y, Huang J, et al. (2000). "Bovine NAD+-dependent isocitrate dehydrogenase: alternative splicing and tissue-dependent expression of subunit 1". Biochemistry. 39 (7): 1807–16. doi:10.1021/bi991691i. PMID 10677231.
  • Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
  • Adkins JN, Varnum SM, Auberry KJ, et al. (2003). "Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry". Mol. Cell. Proteomics. 1 (12): 947–55. doi:10.1074/mcp.M200066-MCP200. PMID 12543931.
  • Soundar S, Park JH, Huh TL, Colman RF (2004). "Evaluation by mutagenesis of the importance of 3 arginines in alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase". J. Biol. Chem. 278 (52): 52146–53. doi:10.1074/jbc.M306178200. PMID 14555658.
  • Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40–5. doi:10.1038/ng1285. PMID 14702039.
  • Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
  • Guo D, Han J, Adam BL, et al. (2005). "Proteomic analysis of SUMO4 substrates in HEK293 cells under serum starvation-induced stress". Biochem. Biophys. Res. Commun. 337 (4): 1308–18. doi:10.1016/j.bbrc.2005.09.191. PMID 16236267.
  • Soundar S, O'hagan M, Fomulu KS, Colman RF (2006). "Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase". J. Biol. Chem. 281 (30): 21073–81. doi:10.1074/jbc.M602956200. PMID 16737955.
  • Bzymek KP, Colman RF (2007). "Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase". Biochemistry. 46 (18): 5391–7. doi:10.1021/bi700061t. PMID 17432878.
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