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IDH3B isocitrate dehydrogenase 3 (NAD(+)) beta [ Homo sapiens (human) ]

Gene ID: 3420, updated on 4-Nov-2018

Summary

Official Symbol
IDH3Bprovided by HGNC
Official Full Name
isocitrate dehydrogenase 3 (NAD(+)) betaprovided by HGNC
Primary source
HGNC:HGNC:5385
See related
Ensembl:ENSG00000101365 MIM:604526; Vega:OTTHUMG00000031699
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

Genomic context

See IDH3B in Genome Data Viewer
Location:
20p13
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (2658390..2664223, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2639041..2644865, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NOP56 ribonucleoprotein Neighboring gene small nucleolar RNA, C/D box 56 Neighboring gene small nucleolar RNA, C/D box 57 Neighboring gene uncharacterized LOC105372507 Neighboring gene uncharacterized LOC105372506 Neighboring gene EBF family member 4

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • 2-Oxocarboxylic acid metabolism, organism-specific biosystem (from KEGG)
    2-Oxocarboxylic acid metabolism, organism-specific biosystem2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate)...
  • 2-Oxocarboxylic acid metabolism, conserved biosystem (from KEGG)
    2-Oxocarboxylic acid metabolism, conserved biosystem2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate)...
  • Biosynthesis of amino acids, organism-specific biosystem (from KEGG)
    Biosynthesis of amino acids, organism-specific biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Biosynthesis of amino acids, conserved biosystem (from KEGG)
    Biosynthesis of amino acids, conserved biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Carbon metabolism, organism-specific biosystem (from KEGG)
    Carbon metabolism, organism-specific biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Carbon metabolism, conserved biosystem (from KEGG)
    Carbon metabolism, conserved biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Citrate cycle (TCA cycle), organism-specific biosystem (from KEGG)
    Citrate cycle (TCA cycle), organism-specific biosystemThe citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form ...
  • Citrate cycle (TCA cycle), conserved biosystem (from KEGG)
    Citrate cycle (TCA cycle), conserved biosystemThe citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form ...
  • Citrate cycle (TCA cycle, Krebs cycle), organism-specific biosystem (from KEGG)
    Citrate cycle (TCA cycle, Krebs cycle), organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Citrate cycle (TCA cycle, Krebs cycle), conserved biosystem (from KEGG)
    Citrate cycle (TCA cycle, Krebs cycle), conserved biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, organism-specific biosystem (from KEGG)
    Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, conserved biosystem (from KEGG)
    Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
  • Citric acid cycle (TCA cycle), organism-specific biosystem (from REACTOME)
    Citric acid cycle (TCA cycle), organism-specific biosystemIn the citric acid or tricarboxylic acid (TCA) cycle, the acetyl group of acetyl CoA (derived primarily from oxidative decarboxylation of pyruvate, beta-oxidation of long-chain fatty acids, and catab...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Pyruvate metabolism and Citric Acid (TCA) cycle, organism-specific biosystem (from REACTOME)
    Pyruvate metabolism and Citric Acid (TCA) cycle, organism-specific biosystemPyruvate metabolism and the citric acid (TCA) cycle together link the processes of energy metabolism in a human cell with one another and with key biosynthetic reactions. Pyruvate, derived from the r...
  • TCA Cycle, organism-specific biosystem (from WikiPathways)
    TCA Cycle, organism-specific biosystemThe [[wikipedia:citric_acid_cycle|citric acid cycle]], also known as the tricarboxylic acid cycle (TCA cycle) or the Krebs cycle, (or rarely, the Szent-Gyorgyi-Krebs cycle) is a series of enzyme-cata...
  • The citric acid (TCA) cycle and respiratory electron transport, organism-specific biosystem (from REACTOME)
    The citric acid (TCA) cycle and respiratory electron transport, organism-specific biosystemThe metabolism of pyruvate provides one source of acetyl-CoA which enters the citric acid (TCA, tricarboxylic acid) cycle to generate energy and the reducing equivalent NADH. These reducing equivalen...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC903, FLJ11043

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NAD binding IEA
Inferred from Electronic Annotation
more info
 
electron transfer activity TAS
Traceable Author Statement
more info
PubMed 
isocitrate dehydrogenase (NAD+) activity IEA
Inferred from Electronic Annotation
more info
 
magnesium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
electron transport chain IEA
Inferred from Electronic Annotation
more info
 
isocitrate metabolic process TAS
Traceable Author Statement
more info
PubMed 
tricarboxylic acid cycle IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nucleus HDA PubMed 

General protein information

Preferred Names
isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
Names
NAD(+)-specific ICDH subunit 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)

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
    4975..10808
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001258384.2NP_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_001330763.1NP_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/Swiss-Prot
    O43837
    UniProtKB/TrEMBL
    A0A087WZN1
    Related
    ENSP00000482773.1, ENST00000474315.5
  3. NM_006899.4NP_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, BX119223, HY131986
    Consensus CDS
    CCDS13032.1
    UniProtKB/Swiss-Prot
    O43837
    Related
    ENSP00000370223.4, OTTHUMP00000030024, ENST00000380843.8, OTTHUMT00000077613
    Conserved Domains (1) summary
    cl00445
    Location:47380
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase
  4. NM_174855.3NP_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, BX119223, HY131986
    Consensus CDS
    CCDS13031.1
    UniProtKB/Swiss-Prot
    O43837
    Related
    ENSP00000370232.5, OTTHUMP00000030023, ENST00000380851.9, OTTHUMT00000077612
    Conserved Domains (1) summary
    cl00445
    Location:47380
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase

RNA

  1. NR_136344.1 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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

    Range
    2658390..2664223 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001754266.1 RNA Sequence

  2. XR_001754267.1 RNA Sequence

  3. XR_001754265.1 RNA Sequence

    Related
    ENST00000488299.5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_174856.1: Suppressed sequence

    Description
    NM_174856.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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