Human Gene OGDH (uc003tln.3) Description and Page Index
  Description: Homo sapiens oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) (OGDH), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.
RefSeq Summary (NM_002541): 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].
Transcript (Including UTRs)
   Position: hg19 chr7:44,646,121-44,748,669 Size: 102,549 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr7:44,663,943-44,747,598 Size: 83,656 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:44,646,121-44,748,669)mRNA (may differ from genome)Protein (1023 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ODO1_HUMAN
DESCRIPTION: RecName: Full=2-oxoglutarate dehydrogenase, mitochondrial; EC=1.2.4.2; AltName: Full=2-oxoglutarate dehydrogenase complex component E1; Short=OGDC-E1; AltName: Full=Alpha-ketoglutarate dehydrogenase; Flags: Precursor;
FUNCTION: The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2- oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3).
CATALYTIC ACTIVITY: 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2).
COFACTOR: Thiamine pyrophosphate.
ENZYME REGULATION: Catabolite repressed.
SUBCELLULAR LOCATION: Mitochondrion matrix.
SIMILARITY: Belongs to the alpha-ketoglutarate dehydrogenase family.
SEQUENCE CAUTION: Sequence=BAA01393.1; Type=Frameshift; Positions=1003; Sequence=BAA06836.1; Type=Frameshift; Positions=1003;
WEB RESOURCE: Name=Wikipedia; Note=Alpha-ketoglutarate dehydrogenase entry; URL="http://en.wikipedia.org/wiki/Alpha-ketoglutarate_dehydrogenase";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): OGDH
CDC HuGE Published Literature: OGDH

-  MalaCards Disease Associations
  MalaCards Gene Search: OGDH
Diseases sorted by gene-association score: alpha-ketoglutarate dehydrogenase deficiency* (183), door syndrome (10), wernicke-korsakoff syndrome (9), primary biliary cirrhosis (6), lactic acidosis (5), hypotonia (4), autoimmune disease of urogenital tract (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 146.70 RPKM in Heart - Left Ventricle
Total median expression: 1712.70 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -67.60159-0.425 Picture PostScript Text
3' UTR -452.041071-0.422 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011603 - 2oxoglutarate_DH_E1
IPR001017 - DH_E1
IPR005475 - Transketolase-like_Pyr-bd

Pfam Domains:
PF00676 - Dehydrogenase E1 component
PF02779 - Transketolase, pyrimidine binding domain
PF16078 - 2-oxoglutarate dehydrogenase N-terminus
PF16870 - 2-oxoglutarate dehydrogenase C-terminal

SCOP Domains:
52518 - Thiamin diphosphate-binding fold (THDP-binding)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3ERY
- X-ray


ModBase Predicted Comparative 3D Structure on Q02218
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
GO:0016491 oxidoreductase activity
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0030976 thiamine pyrophosphate binding
GO:0031072 heat shock protein binding
GO:0034602 oxoglutarate dehydrogenase (NAD+) activity
GO:0046872 metal ion binding
GO:0051087 chaperone binding

Biological Process:
GO:0006091 generation of precursor metabolites and energy
GO:0006096 glycolytic process
GO:0006099 tricarboxylic acid cycle
GO:0006103 2-oxoglutarate metabolic process
GO:0006104 succinyl-CoA metabolic process
GO:0006734 NADH metabolic process
GO:0008152 metabolic process
GO:0021695 cerebellar cortex development
GO:0021756 striatum development
GO:0021766 hippocampus development
GO:0021794 thalamus development
GO:0021860 pyramidal neuron development
GO:0022028 tangential migration from the subventricular zone to the olfactory bulb
GO:0055114 oxidation-reduction process
GO:0061034 olfactory bulb mitral cell layer development

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0031966 mitochondrial membrane
GO:0045252 oxoglutarate dehydrogenase complex
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF384709 - JP 2014500723-A/192212: Polycomb-Associated Non-Coding RNAs.
AK296400 - Homo sapiens cDNA FLJ59557 complete cds, highly similar to 2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2).
BC009580 - Homo sapiens oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide), mRNA (cDNA clone IMAGE:4046929), complete cds.
AK304439 - Homo sapiens cDNA FLJ54748 complete cds, highly similar to 2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2).
AK314179 - Homo sapiens cDNA, FLJ94900.
D10523 - Homo sapiens mRNA for 2-oxoglutarate dehydrogenase, complete cds.
BC004964 - Homo sapiens oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide), mRNA (cDNA clone MGC:1693 IMAGE:3528538), complete cds.
BC014617 - Homo sapiens oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide), mRNA (cDNA clone MGC:3684 IMAGE:3010095), complete cds.
HM005444 - Homo sapiens clone HTL-T-131 testicular tissue protein Li 131 mRNA, complete cds.
CU679409 - Synthetic construct Homo sapiens gateway clone IMAGE:100019346 5' read OGDH mRNA.
CU678824 - Synthetic construct Homo sapiens gateway clone IMAGE:100020536 5' read OGDH mRNA.
KJ905845 - Synthetic construct Homo sapiens clone ccsbBroadEn_15515 OGDH gene, encodes complete protein.
AB384689 - Synthetic construct DNA, clone: pF1KB0207, Homo sapiens OGDH gene for oxoglutarate dehydrogenase, complete cds, without stop codon, in Flexi system.
EU176648 - Synthetic construct Homo sapiens clone IMAGE:100011445; FLH180883.01L; RZPDo839E10254D oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) (OGDH) gene, encodes complete protein.
DQ891880 - Synthetic construct clone IMAGE:100004510; FLH180884.01X; RZPDo839H01134D oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) (OGDH) gene, encodes complete protein.
AK304690 - Homo sapiens cDNA FLJ59657 complete cds, highly similar to 2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2).
AK293871 - Homo sapiens cDNA FLJ53308 complete cds, highly similar to 2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2).
AK302805 - Homo sapiens cDNA FLJ54570 complete cds, highly similar to 2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2).
BC128550 - Homo sapiens oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide), mRNA (cDNA clone IMAGE:40121617), partial cds.
BC128549 - Homo sapiens oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide), mRNA (cDNA clone IMAGE:40121616), partial cds.
DQ925673 - Homo sapiens clone 1B-3 oxoglutarate (alpha-ketoglutarate) dehydrogenase (OGDH) mRNA, partial cds, alternatively spliced.
DQ925674 - Homo sapiens clone 1B-2 oxoglutarate (alpha-ketoglutarate) dehydrogenase (OGDH) mRNA, partial cds, alternatively spliced.
MA620286 - JP 2018138019-A/192212: Polycomb-Associated Non-Coding RNAs.
LF208993 - JP 2014500723-A/16496: Polycomb-Associated Non-Coding RNAs.
LF324865 - JP 2014500723-A/132368: Polycomb-Associated Non-Coding RNAs.
LF324874 - JP 2014500723-A/132377: Polycomb-Associated Non-Coding RNAs.
MA560442 - JP 2018138019-A/132368: Polycomb-Associated Non-Coding RNAs.
MA560451 - JP 2018138019-A/132377: Polycomb-Associated Non-Coding RNAs.
MA444570 - JP 2018138019-A/16496: Polycomb-Associated Non-Coding RNAs.
AK294951 - Homo sapiens cDNA FLJ53323 complete cds, highly similar to 2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2).
LF324880 - JP 2014500723-A/132383: Polycomb-Associated Non-Coding RNAs.
LF324882 - JP 2014500723-A/132385: Polycomb-Associated Non-Coding RNAs.
LF324883 - JP 2014500723-A/132386: Polycomb-Associated Non-Coding RNAs.
LF324885 - JP 2014500723-A/132388: Polycomb-Associated Non-Coding RNAs.
LF324886 - JP 2014500723-A/132389: Polycomb-Associated Non-Coding RNAs.
LF324890 - JP 2014500723-A/132393: Polycomb-Associated Non-Coding RNAs.
LF324891 - JP 2014500723-A/132394: Polycomb-Associated Non-Coding RNAs.
LF324892 - JP 2014500723-A/132395: Polycomb-Associated Non-Coding RNAs.
JD221076 - Sequence 202100 from Patent EP1572962.
JD192484 - Sequence 173508 from Patent EP1572962.
JD391367 - Sequence 372391 from Patent EP1572962.
JD399287 - Sequence 380311 from Patent EP1572962.
JD364265 - Sequence 345289 from Patent EP1572962.
JD499325 - Sequence 480349 from Patent EP1572962.
JD157180 - Sequence 138204 from Patent EP1572962.
LF324893 - JP 2014500723-A/132396: Polycomb-Associated Non-Coding RNAs.
JD547538 - Sequence 528562 from Patent EP1572962.
JD152616 - Sequence 133640 from Patent EP1572962.
LF324894 - JP 2014500723-A/132397: Polycomb-Associated Non-Coding RNAs.
JD241372 - Sequence 222396 from Patent EP1572962.
JD206146 - Sequence 187170 from Patent EP1572962.
JD508263 - Sequence 489287 from Patent EP1572962.
JD456167 - Sequence 437191 from Patent EP1572962.
LF324895 - JP 2014500723-A/132398: Polycomb-Associated Non-Coding RNAs.
JD395919 - Sequence 376943 from Patent EP1572962.
JD045468 - Sequence 26492 from Patent EP1572962.
JD526381 - Sequence 507405 from Patent EP1572962.
LF324896 - JP 2014500723-A/132399: Polycomb-Associated Non-Coding RNAs.
JD078162 - Sequence 59186 from Patent EP1572962.
JD467477 - Sequence 448501 from Patent EP1572962.
JD209798 - Sequence 190822 from Patent EP1572962.
JD333881 - Sequence 314905 from Patent EP1572962.
JD270636 - Sequence 251660 from Patent EP1572962.
JD114951 - Sequence 95975 from Patent EP1572962.
JD189297 - Sequence 170321 from Patent EP1572962.
JD262280 - Sequence 243304 from Patent EP1572962.
JD487783 - Sequence 468807 from Patent EP1572962.
JD256235 - Sequence 237259 from Patent EP1572962.
JD498887 - Sequence 479911 from Patent EP1572962.
JD262925 - Sequence 243949 from Patent EP1572962.
JD068794 - Sequence 49818 from Patent EP1572962.
JD533550 - Sequence 514574 from Patent EP1572962.
JD216384 - Sequence 197408 from Patent EP1572962.
JD455376 - Sequence 436400 from Patent EP1572962.
JD200241 - Sequence 181265 from Patent EP1572962.
LF324897 - JP 2014500723-A/132400: Polycomb-Associated Non-Coding RNAs.
MA560457 - JP 2018138019-A/132383: Polycomb-Associated Non-Coding RNAs.
MA560459 - JP 2018138019-A/132385: Polycomb-Associated Non-Coding RNAs.
MA560460 - JP 2018138019-A/132386: Polycomb-Associated Non-Coding RNAs.
MA560462 - JP 2018138019-A/132388: Polycomb-Associated Non-Coding RNAs.
MA560463 - JP 2018138019-A/132389: Polycomb-Associated Non-Coding RNAs.
MA560467 - JP 2018138019-A/132393: Polycomb-Associated Non-Coding RNAs.
MA560468 - JP 2018138019-A/132394: Polycomb-Associated Non-Coding RNAs.
MA560469 - JP 2018138019-A/132395: Polycomb-Associated Non-Coding RNAs.
MA560470 - JP 2018138019-A/132396: Polycomb-Associated Non-Coding RNAs.
MA560471 - JP 2018138019-A/132397: Polycomb-Associated Non-Coding RNAs.
MA560472 - JP 2018138019-A/132398: Polycomb-Associated Non-Coding RNAs.
MA560473 - JP 2018138019-A/132399: Polycomb-Associated Non-Coding RNAs.
MA560474 - JP 2018138019-A/132400: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00020 - Citrate cycle (TCA cycle)
hsa00310 - Lysine degradation
hsa00380 - Tryptophan metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
LYSINE-DEG1-PWY - lysine degradation II
PWY-5084 - 2-ketoglutarate dehydrogenase complex
PWY-5652 - 2-amino-3-carboxymuconate semialdehyde degradation to glutaryl-CoA
TRYPTOPHAN-DEGRADATION-1 - tryptophan degradation III (eukaryotic)

Reactome (by CSHL, EBI, and GO)

Protein Q02218 (Reactome details) participates in the following event(s):

R-HSA-6792572 LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs
R-HSA-71037 alpha-ketoadipate + CoASH + NAD+ => glutaryl-CoA + CO2 + NADH + H+
R-HSA-71401 alpha-ketoglutarate + CoASH + NAD+ => succinyl-CoA + CO2 + NADH + H+
R-HSA-389661 Glyoxylate metabolism and glycine degradation
R-HSA-71064 Lysine catabolism
R-HSA-71403 Citric acid cycle (TCA cycle)
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-6788656 Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle
R-HSA-1430728 Metabolism
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport

-  Other Names for This Gene
  Alternate Gene Symbols: B4E2U9, D3DVL0, E9PBM1, NM_002541, NP_002532, ODO1_HUMAN, Q02218, Q96DD3, Q9UDX0
UCSC ID: uc003tln.3
RefSeq Accession: NM_002541
Protein: Q02218 (aka ODO1_HUMAN)
CCDS: CCDS34627.1, CCDS55107.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002541.3
exon count: 23CDS single in 3' UTR: no RNA size: 4319
ORF size: 3072CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6344.00frame shift in genome: no % Coverage: 99.61
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.