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OGDH oxoglutarate dehydrogenase [ Homo sapiens (human) ]

Gene ID: 4967, updated on 12-Aug-2018

Summary

Official Symbol
OGDHprovided by HGNC
Official Full Name
oxoglutarate dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:8124
See related
Ensembl:ENSG00000105953 MIM:613022; Vega:OTTHUMG00000155304
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; OGDC; AKGDH
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

Genomic context

See OGDH in Genome Data Viewer
Location:
7p13
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (44606522..44709070)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44646104..44748669)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene DEAD-box helicase 56 Neighboring gene transmembrane p24 trafficking protein 4 Neighboring gene OGDH intron CAGE-defined high expression enhancer Neighboring gene zinc finger MIZ-type containing 2 Neighboring gene uncharacterized LOC105375259 Neighboring gene peptidylprolyl isomerase A

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?

HIV-1 interactions

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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chaperone binding IEA
Inferred from Electronic Annotation
more info
 
heat shock protein binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
oxoglutarate dehydrogenase (NAD+) activity IEA
Inferred from Electronic Annotation
more info
 
oxoglutarate dehydrogenase (succinyl-transferring) activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
oxoglutarate dehydrogenase (succinyl-transferring) activity IDA
Inferred from Direct Assay
more info
PubMed 
oxoglutarate dehydrogenase (succinyl-transferring) activity ISS
Inferred from Sequence or Structural Similarity
more info
 
thiamine pyrophosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
2-oxoglutarate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
NADH metabolic process IEA
Inferred from Electronic Annotation
more info
 
cerebellar cortex development IEA
Inferred from Electronic Annotation
more info
 
generation of precursor metabolites and energy ISS
Inferred from Sequence or Structural Similarity
more info
 
glycolytic process IEA
Inferred from Electronic Annotation
more info
 
hippocampus development IEA
Inferred from Electronic Annotation
more info
 
histone succinylation IDA
Inferred from Direct Assay
more info
PubMed 
olfactory bulb mitral cell layer development IEA
Inferred from Electronic Annotation
more info
 
pyramidal neuron development IEA
Inferred from Electronic Annotation
more info
 
striatum development IEA
Inferred from Electronic Annotation
more info
 
succinyl-CoA metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
tangential migration from the subventricular zone to the olfactory bulb IEA
Inferred from Electronic Annotation
more info
 
thalamus development IEA
Inferred from Electronic Annotation
more info
 
tricarboxylic acid cycle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrial membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
oxoglutarate dehydrogenase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
oxoglutarate dehydrogenase complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
2-oxoglutarate dehydrogenase, mitochondrial
Names
2-oxoglutarate dehydrogenase complex component E1
OGDC-E1
oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)
oxoglutarate decarboxylase
oxoglutarate dehydrogenase (succinyl-transferring)
testicular tissue protein Li 131
NP_001003941.1
NP_001158508.1
NP_002532.2
XP_005249816.1
XP_005249818.1
XP_011513710.1
XP_024302551.1

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_023260.1 RefSeqGene

    Range
    5001..107549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001003941.2NP_001003941.1  2-oxoglutarate dehydrogenase, mitochondrial 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, BM998792, DC401267
    Consensus CDS
    CCDS47580.1
    UniProtKB/Swiss-Prot
    Q02218
    UniProtKB/TrEMBL
    A0A140VJQ5
    Related
    ENSP00000388084.2, OTTHUMP00000207708, ENST00000443864.6, OTTHUMT00000339397
    Conserved Domains (1) summary
    cl25580
    Location:49405
    OxoGdeHyase_C; 2-oxoglutarate dehydrogenase C-terminal
  2. NM_001165036.1NP_001158508.1  2-oxoglutarate dehydrogenase, mitochondrial 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, DC401267
    Consensus CDS
    CCDS55107.1
    UniProtKB/Swiss-Prot
    Q02218
    UniProtKB/TrEMBL
    B4E3E9
    Related
    ENSP00000392878.1, OTTHUMP00000207704, ENST00000449767.5, OTTHUMT00000339392
    Conserved Domains (1) summary
    PRK09404
    Location:491011
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
  3. NM_001363523.1NP_001350452.1  2-oxoglutarate dehydrogenase, mitochondrial isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC004859, AC011894
    Consensus CDS
    CCDS87498.1
    Conserved Domains (1) summary
    PRK09404
    Location:491026
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
  4. NM_002541.3NP_002532.2  2-oxoglutarate dehydrogenase, mitochondrial 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, DC401267
    Consensus CDS
    CCDS34627.1
    UniProtKB/Swiss-Prot
    Q02218
    UniProtKB/TrEMBL
    B4E3E9
    Related
    ENSP00000222673.5, OTTHUMP00000207703, ENST00000222673.5, OTTHUMT00000339391
    Conserved Domains (1) summary
    PRK09404
    Location:491015
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed

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_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    44606522..44709070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005249761.3XP_005249818.1  2-oxoglutarate dehydrogenase, mitochondrial isoform X2

    UniProtKB/TrEMBL
    E9PDF2
    Related
    ENSP00000388183.1, OTTHUMP00000207705, ENST00000447398.5, OTTHUMT00000339393
    Conserved Domains (1) summary
    PRK09404
    Location:491026
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
  2. XM_005249759.5XP_005249816.1  2-oxoglutarate dehydrogenase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_005249816.1

    UniProtKB/TrEMBL
    E9PCR7
    Related
    ENSP00000414662.1, OTTHUMP00000207707, ENST00000444676.5
    Conserved Domains (1) summary
    PRK09404
    Location:491030
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
  3. XM_011515408.2XP_011513710.1  2-oxoglutarate dehydrogenase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011513710.1

    UniProtKB/TrEMBL
    E9PCR7
    Conserved Domains (1) summary
    PRK09404
    Location:491030
    sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
  4. XM_024446783.1XP_024302551.1  2-oxoglutarate dehydrogenase, mitochondrial isoform X3

    Related
    ENSP00000398576.2, ENST00000439616.6
    Conserved Domains (1) summary
    cl25580
    Location:59810
    OxoGdeHyase_C; 2-oxoglutarate dehydrogenase C-terminal
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