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OGDH oxoglutarate dehydrogenase [ Homo sapiens (human) ]

Gene ID: 4967, updated on 11-Apr-2024

Summary

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Official Symbol
OGDHprovided by HGNC
Official Full Name
oxoglutarate dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:8124
See related
Ensembl:ENSG00000105953 MIM:613022; AllianceGenome:HGNC:8124
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
E1k; E1o; KGD1; OGDC; AKGDH; OGDH2; OGDHD; OGDH-E1
Summary
This gene encodes one subunit of the 2-oxoglutarate dehydrogenase complex. This complex catalyzes the overall conversion of 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA and CO(2) during the Krebs cycle. The protein is located in the mitochondrial matrix and uses thiamine pyrophosphate as a cofactor. A congenital deficiency in 2-oxoglutarate dehydrogenase activity is believed to lead to hypotonia, metabolic acidosis, and hyperlactatemia. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Sep 2009]
Expression
Ubiquitous expression in heart (RPKM 71.3), kidney (RPKM 57.5) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
7p13
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44606627..44709066)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44766778..44869231)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44646226..44748665)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44605263-44605762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25943 Neighboring gene DEAD-box helicase 56 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25944 Neighboring gene transmembrane p24 trafficking protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44646637-44647200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25949 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44674956-44675111 Neighboring gene OGDH intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25951 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:44679045-44679572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44685039-44685539 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44717745-44717958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44740093-44740593 Neighboring gene uncharacterized LOC124901622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44794273-44794954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44807583-44808109 Neighboring gene zinc finger MIZ-type containing 2

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. Hypoxic regulation of glutamine metabolism through HIF1 and SIAH2 supports lipid synthesis that is necessary for tumor growth. Sun RC, et al. Cell Metab, 2014 Feb 4. PMID 24506869, Free PMC Article
  2. Exercise training induces similar elevations in the activity of oxoglutarate dehydrogenase and peak oxygen uptake in the human quadriceps muscle. Blomstrand E, et al. Pflugers Arch, 2011 Aug. PMID 21611730
  3. Reduction in the E2k subunit of the alpha-ketoglutarate dehydrogenase complex has effects independent of complex activity. Shi Q, et al. J Biol Chem, 2005 Mar 25. PMID 15649899
  4. Localization of the gene (OGDH) coding for the E1k component of the alpha-ketoglutarate dehydrogenase complex to chromosome 7p13-p11.2. Szabo P, et al. Genomics, 1994 Mar 15. PMID 8020988
  5. The gene encoding human 2-oxoglutarate dehydrogenase: structural organization and mapping to chromosome 7p13-p14. Koike K. Gene, 1995 Jul 4. PMID 7622061

See all (102) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Biallelic variants in OGDH encoding oxoglutarate dehydrogenase lead to a neurodevelopmental disorder characterized by global developmental delay, movement disorder, and metabolic abnormalities.
    Title: Biallelic variants in OGDH encoding oxoglutarate dehydrogenase lead to a neurodevelopmental disorder characterized by global developmental delay, movement disorder, and metabolic abnormalities.
  2. A biallelic pathogenic variant in the OGDH gene results in a neurological disorder with features of a mitochondrial disease.
    Title: A biallelic pathogenic variant in the OGDH gene results in a neurological disorder with features of a mitochondrial disease.
  3. DHTKD1 and OGDH display substrate overlap in cultured cells and form a hybrid 2-oxo acid dehydrogenase complex in vivo.
    Title: DHTKD1 and OGDH display substrate overlap in cultured cells and form a hybrid 2-oxo acid dehydrogenase complex in vivo.
  4. Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues.
    Title: Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues.
  5. there is the direct interaction between SIRT5 and 2-oxoglutarate dehydrogenase (OGDH), and desuccinylation of OGDH by SIRT5 inhibits the activity of OGDH complex.
    Title: OGDH mediates the inhibition of SIRT5 on cell proliferation and migration of gastric cancer.
  6. The data indicate that amino acid/nucleotide metabolism-related genes OGDH, PPAT and PCCA acquire somatic mutations in microsatellite instability-high gastric cancers and colorectal cancers and that mutational intratumoral heterogeneity may occur in at least some of these tumors.
    Title: Frameshift mutations of OGDH, PPAT and PCCA genes in gastric and colorectal cancers.
  7. PIK3CA mutant cancer cells require PIK3CA but also require the expression of the TCA cycle enzyme 2-oxoglutarate dehydrogenase (OGDH).
    Title: PIK3CA mutant tumors depend on oxoglutarate dehydrogenase.
  8. oxoglutarate dehydrogenase (OGDH) and lipoic acid synthase (LIAS), which when mutated stabilize HIF1alpha in a non-hydroxylated form.
    Title: Mitochondrial Protein Lipoylation and the 2-Oxoglutarate Dehydrogenase Complex Controls HIF1α Stability in Aerobic Conditions.
  9. Tissue-specific expression of OGDH splice variants may thus provide a mechanism that tunes the control of the enzyme to the specialized metabolic and signalling needs of individual cell types
    Title: Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression.
  10. ATP consumption is demonstrated in respiration-impaired isolated mice and in situ neuronal mitochondria from transgenic mice with dihydrolipoyl succinyltransferase deficiency.
    Title: The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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

Associated conditions

Description Tests
Oxoglutaricaciduria
MedGen: C2752074 OMIM: 203740 GeneReviews: Not available
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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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Protein interactions

Protein Gene Interaction Pubs
Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of oxoglutarate (alpha-ketoglutarate) dehydrogenase (OGDH) expression by HIV-1 Vpr in Vpr transduced macrophages 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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxoglutarate dehydrogenase (NAD+) activity IEA
Inferred from Electronic Annotation
more info
  
enables oxoglutarate dehydrogenase (succinyl-transferring) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables oxoglutarate dehydrogenase (succinyl-transferring) activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables oxoglutarate dehydrogenase (succinyl-transferring) activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables thiamine pyrophosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in 2-oxoglutarate metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cerebellar cortex development IEA
Inferred from Electronic Annotation
more info
  
involved_in generation of precursor metabolites and energy ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in glycolytic process IEA
Inferred from Electronic Annotation
more info
  
involved_in hippocampus development IEA
Inferred from Electronic Annotation
more info
  
involved_in olfactory bulb mitral cell layer development IEA
Inferred from Electronic Annotation
more info
  
involved_in pyramidal neuron development IEA
Inferred from Electronic Annotation
more info
  
involved_in striatum development IEA
Inferred from Electronic Annotation
more info
  
involved_in succinyl-CoA metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tangential migration from the subventricular zone to the olfactory bulb IEA
Inferred from Electronic Annotation
more info
  
involved_in thalamus development IEA
Inferred from Electronic Annotation
more info
  
involved_in tricarboxylic acid cycle IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrial membrane ISS
Inferred from Sequence or Structural Similarity
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
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of oxoglutarate dehydrogenase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of oxoglutarate dehydrogenase complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
2-oxoglutarate dehydrogenase complex component E1
Names
2-oxoglutarate dehydrogenase, mitochondrial
OGDC-E1
alpha-KGDH-E1
oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)
oxoglutarate decarboxylase
oxoglutarate dehydrogenase (succinyl-transferring)
testicular tissue protein Li 131
thiamine diphosphate (ThDP)-dependent 2-oxoglutarate dehydrogenase
NP_001003941.1
NP_001158508.1
NP_001350452.1
NP_002532.2
XP_005249816.1
XP_011513710.1
XP_047276382.1
XP_047276383.1
XP_047276384.1
XP_047276385.1
XP_054214282.1
XP_054214283.1
XP_054214284.1
XP_054214285.1
XP_054214286.1
XP_054214287.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_023260.1 RefSeqGene

    Range
    5106..107545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001003941.3 → NP_001003941.1  2-oxoglutarate dehydrogenase complex component E1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001003941.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' end of coding region, compared to variant 1. Variant 2 encodes isoform 2 which has a shorter and distinct C-terminus, compared to isoform 1. Variant 2 is supported by transcriptional evidence although the protein product is predicted.
    Source sequence(s)
    BC009580
    Consensus CDS
    CCDS47580.1
    UniProtKB/TrEMBL
    A0A140VJQ5
    Related
    ENSP00000388084.2, ENST00000443864.6
    Conserved Domains (1) summary
    cl25580
    Location:49 → 405
    OxoGdeHyase_C; 2-oxoglutarate dehydrogenase C-terminal

  2. NM_001165036.2 → NP_001158508.1  2-oxoglutarate dehydrogenase complex component E1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001158508.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the presence and absence of exons in the 5' coding region, compared to variant 1. These differences result in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AC004859, AK304439, AK304690, BU682361
    Consensus CDS
    CCDS55107.1
    UniProtKB/TrEMBL
    B4DF00
    Related
    ENSP00000392878.1, ENST00000449767.5
    Conserved Domains (1) summary
    PRK09404
    Location:49 → 1011
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed

  3. NM_001363523.2 → NP_001350452.1  2-oxoglutarate dehydrogenase complex component E1 isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC004859, AC011894
    Consensus CDS
    CCDS87498.1
    UniProtKB/TrEMBL
    B4DF00, E9PDF2
    Related
    ENSP00000388183.1, ENST00000447398.6
    Conserved Domains (1) summary
    PRK09404
    Location:49 → 1026
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed

  4. NM_002541.4 → NP_002532.2  2-oxoglutarate dehydrogenase complex component E1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002532.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC004859, AK304690, AK314179, BU682361
    Consensus CDS
    CCDS34627.1
    UniProtKB/Swiss-Prot
    B4E2U9, D3DVL0, E9PBM1, Q02218, Q96DD3, Q9UDX0
    UniProtKB/TrEMBL
    B4DF00
    Related
    ENSP00000222673.5, ENST00000222673.6
    Conserved Domains (1) summary
    PRK09404
    Location:49 → 1015
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    44606627..44709066
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420428.1 → XP_047276384.1  2-oxoglutarate dehydrogenase complex component E1 isoform X3

  2. XM_011515408.3 → XP_011513710.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

    See identical proteins and their annotated locations for XP_011513710.1

    UniProtKB/TrEMBL
    B4DF00, E9PCR7
    Conserved Domains (1) summary
    PRK09404
    Location:49 → 1030
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed

  3. XM_047420427.1 → XP_047276383.1  2-oxoglutarate dehydrogenase complex component E1 isoform X2

    UniProtKB/Swiss-Prot
    B4E2U9, D3DVL0, E9PBM1, Q02218, Q96DD3, Q9UDX0

  4. XM_005249759.6 → XP_005249816.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

    See identical proteins and their annotated locations for XP_005249816.1

    UniProtKB/TrEMBL
    B4DF00, E9PCR7
    Related
    ENSP00000414662.1, ENST00000444676.5
    Conserved Domains (1) summary
    PRK09404
    Location:49 → 1030
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed

  5. XM_047420426.1 → XP_047276382.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

    UniProtKB/TrEMBL
    E9PCR7

  6. XM_047420429.1 → XP_047276385.1  2-oxoglutarate dehydrogenase complex component E1 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    44766778..44869231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358311.1 → XP_054214286.1  2-oxoglutarate dehydrogenase complex component E1 isoform X3

  2. XM_054358308.1 → XP_054214283.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

  3. XM_054358310.1 → XP_054214285.1  2-oxoglutarate dehydrogenase complex component E1 isoform X2

  4. XM_054358307.1 → XP_054214282.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

  5. XM_054358309.1 → XP_054214284.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

  6. XM_054358312.1 → XP_054214287.1  2-oxoglutarate dehydrogenase complex component E1 isoform X4

    UniProtKB/TrEMBL
    B4DH65
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q02218.3 GenPept UniProtKB/Swiss-Prot:Q02218

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