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IDH3G isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [ Homo sapiens (human) ]

Gene ID: 3421, updated on 11-Apr-2024

Summary

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Official Symbol
IDH3Gprovided by HGNC
Official Full Name
isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gammaprovided by HGNC
Primary source
HGNC:HGNC:5386
See related
Ensembl:ENSG00000067829 MIM:300089; AllianceGenome:HGNC:5386
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
H-IDHG
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. 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 gamma subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. This gene is a candidate gene for periventricular heterotopia. Several alternatively spliced transcript variants of this gene have been described, but only some of their full length natures have been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in kidney (RPKM 22.6), heart (RPKM 18.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
Xq28
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153785768..153794375, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152059431..152068038, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153051223..153059830, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene PLXNB3 antisense RNA 1 Neighboring gene plexin B3 Neighboring gene uncharacterized LOC124905227 Neighboring gene SRSF protein kinase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153059193-153059920 Neighboring gene CRISPRi-validated cis-regulatory element chrX.2654 Neighboring gene signal sequence receptor subunit 4 Neighboring gene PDZ domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21072 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:153092379-153092957 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153099642-153099888 Neighboring gene CYCS pseudogene 45

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase. Bzymek KP, et al. Biochemistry, 2007 May 8. PMID 17432878
  2. Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase. Soundar S, et al. J Biol Chem, 2006 Jul 28. PMID 16737955
  3. Identification and functional characterization of a novel, tissue-specific NAD(+)-dependent isocitrate dehydrogenase beta subunit isoform. Kim YO, et al. J Biol Chem, 1999 Dec 24. PMID 10601238
  4. Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase. Ma T, et al. Sci Rep, 2017 Jan 18. PMID 28098230, Free PMC Article
  5. Bovine NAD+-dependent isocitrate dehydrogenase: alternative splicing and tissue-dependent expression of subunit 1. Weiss C, et al. Biochemistry, 2000 Feb 22. PMID 10677231

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. active sites of the human NAD-IDH are shared between alpha and gamma subunits and between alpha and beta subunits
    Title: Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase.
  2. Aspartate-190 is a determinant of IDH gamma subunit affinity for the manganese (MnII) ion, as well as for nicotinamide-adenine dinucleotide (NAD), but is not directly required for the catalytic reaction.
    Title: Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of IDH3G by shRNA significantly inhibits HIV-1 replication in CD4+ T-cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies IDH3G, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables NAD binding IEA
Inferred from Electronic Annotation
more info
  
enables isocitrate dehydrogenase (NAD+) activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables magnesium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in carbohydrate metabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in isocitrate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in isocitrate metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in tricarboxylic acid cycle IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tricarboxylic acid cycle IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of isocitrate dehydrogenase complex (NAD+) IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in mitochondrion NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
Names
IDH-gamma
NAD (H)-specific isocitrate dehydrogenase gamma subunit
NAD(+)-specific ICDH subunit gamma
NAD+-specific ICDH
isocitrate dehydrogenase (NAD(+)) 3 gamma
isocitrate dehydrogenase 3 (NAD(+)) gamma
isocitrate dehydrogenase 3 (NAD+) gamma
isocitrate dehydrogenase 3 gamma
isocitrate dehydrogenase, NAD(+)-specific, mitochondrial, gamma subunit
isocitric dehydrogenase subunit gamma
NP_004126.1
NP_777358.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_004135.4 → NP_004126.1  isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial isoform a precursor

    See identical proteins and their annotated locations for NP_004126.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    BC000933, BI831096
    Consensus CDS
    CCDS14730.1
    UniProtKB/Swiss-Prot
    E9PDD5, P51553, Q9BUU5
    UniProtKB/TrEMBL
    E7EQB8
    Related
    ENSP00000217901.5, ENST00000217901.10
    Conserved Domains (1) summary
    TIGR00175
    Location:52 → 383
    mito_nad_idh; isocitrate dehydrogenase, NAD-dependent, mitochondrial type

  2. NM_174869.3 → NP_777358.1  isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial isoform b precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding region resulting in a frameshift, compared to variant 1. Variant 2 encodes a shorter isoform (b) with a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    BC000933, BI831096, U69268
    Consensus CDS
    CCDS44019.1
    UniProtKB/TrEMBL
    E7EQB8
    Related
    ENSP00000359110.3, ENST00000370092.7
    Conserved Domains (1) summary
    TIGR00175
    Location:52 → 364
    mito_nad_idh; isocitrate dehydrogenase, NAD-dependent, mitochondrial type

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    153785768..153794375 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152059431..152068038 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51553.1 GenPept UniProtKB/Swiss-Prot:P51553

Gene LinkOut

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