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IDH3B isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit beta [ Homo sapiens (human) ]

Gene ID: 3420, updated on 4-Jan-2025

Summary

Official Symbol
IDH3Bprovided by HGNC
Official Full Name
isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit betaprovided by HGNC
Primary source
HGNC:HGNC:5385
See related
Ensembl:ENSG00000101365 MIM:604526; AllianceGenome:HGNC:5385
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
RP46
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 beta subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Sep 2016]
Expression
Ubiquitous expression in heart (RPKM 34.2), kidney (RPKM 31.3) and 25 other tissues See more
Orthologs
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Genomic context

See IDH3B in Genome Data Viewer
Location:
20p13
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2658395..2664216, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2688862..2694697, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2639041..2644862, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NOP56 ribonucleoprotein Neighboring gene MPRA-validated peak4124 silencer Neighboring gene small nucleolar RNA, C/D box 56 Neighboring gene small nucleolar RNA, C/D box 57 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2643139-2643926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2645500-2646285 Neighboring gene IDH3B divergent transcript Neighboring gene uncharacterized LOC105372507

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

General gene information

Clone Names

  • MGC903, FLJ11043

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables NAD binding  
enables electron transfer activity PubMed 
enables isocitrate dehydrogenase (NAD+) activity PubMed 
enables magnesium ion binding  
enables protein binding PubMed 
Process Evidence Code Pubs
involved_in isocitrate metabolic process  
involved_in tricarboxylic acid cycle  
involved_in tricarboxylic acid cycle PubMed 
Component Evidence Code Pubs
part_of isocitrate dehydrogenase complex (NAD+) PubMed 
part_of isocitrate dehydrogenase complex (NAD+) PubMed 
located_in mitochondrial matrix  
located_in mitochondrion PubMed 
is_active_in mitochondrion  
located_in mitochondrion  
located_in mitochondrion PubMed 
located_in nucleus PubMed 

General protein information

Preferred Names
isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
Names
NAD(+)-specific ICDH subunit beta
isocitrate dehydrogenase (NAD(+)) 3 beta
isocitrate dehydrogenase 3 (NAD(+)) beta
isocitrate dehydrogenase 3 (NAD+) beta
isocitric dehydrogenase subunit beta
NP_001245313.1
NP_001317692.1
NP_008830.2
NP_777280.1

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.

Genomic

  1. NG_012149.1 RefSeqGene

    Range
    4982..10803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001258384.3NP_001245313.1  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform d precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AK309488, AL049712, HY131986
    Consensus CDS
    CCDS74696.1
    UniProtKB/TrEMBL
    A0A087X2E5
    Related
    ENSP00000484922.1, ENST00000613370.1
    Conserved Domains (1) summary
    cl00445
    Location:47358
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase
  2. NM_001330763.2NP_001317692.1  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform e precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (e) has a longer C-terminus compared to isoform a.
    Source sequence(s)
    BC001960, BX119223, HY131986
    Consensus CDS
    CCDS82594.1
    UniProtKB/TrEMBL
    A0A087WZN1
    Related
    ENSP00000482773.1, ENST00000474315.5
  3. NM_006899.5NP_008830.2  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform a precursor

    See identical proteins and their annotated locations for NP_008830.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominate transcript and encodes isoform (a).
    Source sequence(s)
    BC001960, HY131986
    Consensus CDS
    CCDS13032.1
    UniProtKB/Swiss-Prot
    B2RDR1, D3DVX2, D3DVX3, O43837, O95106, Q5JXS8, Q9NQ06, Q9NQ07, Q9NUZ0, Q9UEX0, Q9UG99
    Related
    ENSP00000370223.4, ENST00000380843.9
    Conserved Domains (1) summary
    cl00445
    Location:47380
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase
  4. NM_174855.4NP_777280.1  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform b precursor

    See identical proteins and their annotated locations for NP_777280.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a portion of the coding region which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    BC001960, BG745042, HY131986
    Consensus CDS
    CCDS13031.1
    UniProtKB/Swiss-Prot
    O43837
    Related
    ENSP00000370232.5, ENST00000380851.10
    Conserved Domains (1) summary
    cl00445
    Location:47380
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase

RNA

  1. NR_136344.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL049712, BX119223, HY131986

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    2658395..2664216 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001754265.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    2688862..2694697 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008485261.1 RNA Sequence

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