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Protein

Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial

Gene

IDH3A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei115SubstrateBy similarity1
Binding sitei125SubstrateBy similarity1
Binding sitei146SubstrateBy similarity1
Sitei153Critical for catalysisBy similarity1
Sitei200Critical for catalysisBy similarity1
Metal bindingi233Magnesium or manganeseBy similarity1
Binding sitei233SubstrateBy similarity1
Metal bindingi257Magnesium or manganeseBy similarity1
Metal bindingi261Magnesium or manganeseBy similarity1

GO - Molecular functioni

GO - Biological processi

  • carbohydrate metabolic process Source: ProtInc
  • tricarboxylic acid cycle Source: Reactome

Keywordsi

Molecular functionOxidoreductase
Biological processTricarboxylic acid cycle
LigandMagnesium, Manganese, Metal-binding, NAD

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000166411-MONOMER.
ReactomeiR-HSA-71403. Citric acid cycle (TCA cycle).
SABIO-RKiP50213.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC:1.1.1.41)
Alternative name(s):
Isocitric dehydrogenase subunit alpha
NAD(+)-specific ICDH subunit alpha
Gene namesi
Name:IDH3A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

HGNCiHGNC:5384. IDH3A.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial matrix Source: Reactome
  • mitochondrion Source: HPA
  • myelin sheath Source: Ensembl
  • nucleus Source: UniProtKB

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

DisGeNETi3419.
OpenTargetsiENSG00000166411.
PharmGKBiPA29632.

Chemistry databases

DrugBankiDB00157. NADH.

Polymorphism and mutation databases

BioMutaiIDH3A.
DMDMi1708399.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 27MitochondrionCombined sourcesAdd BLAST27
ChainiPRO_000001443628 – 366Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrialAdd BLAST339

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei77N6-succinyllysineBy similarity1
Modified residuei101PhosphothreonineBy similarity1
Modified residuei223N6-acetyllysineBy similarity1
Modified residuei343N6-acetyllysine; alternateCombined sources1
Modified residuei343N6-succinyllysine; alternateBy similarity1
Modified residuei350N6-succinyllysineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP50213.
MaxQBiP50213.
PaxDbiP50213.
PeptideAtlasiP50213.
PRIDEiP50213.

2D gel databases

OGPiP50213.
REPRODUCTION-2DPAGEiIPI00030702.

PTM databases

iPTMnetiP50213.
PhosphoSitePlusiP50213.
SwissPalmiP50213.

Expressioni

Gene expression databases

BgeeiENSG00000166411.
CleanExiHS_IDH3A.
ExpressionAtlasiP50213. baseline and differential.
GenevisibleiP50213. HS.

Organism-specific databases

HPAiHPA041465.
HPA062971.

Interactioni

Subunit structurei

Heterooligomer of subunits alpha, beta, and gamma in the apparent ratio of 2:1:1.By similarity

Protein-protein interaction databases

BioGridi109645. 51 interactors.
IntActiP50213. 10 interactors.
MINTiMINT-1148360.
STRINGi9606.ENSP00000299518.

Structurei

Secondary structure

1366
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi32 – 37Combined sources6
Helixi43 – 56Combined sources14
Beta strandi60 – 65Combined sources6
Helixi82 – 91Combined sources10
Beta strandi93 – 96Combined sources4
Helixi110 – 118Combined sources9
Beta strandi122 – 128Combined sources7
Beta strandi131 – 133Combined sources3
Beta strandi141 – 147Combined sources7
Beta strandi149 – 151Combined sources3
Beta strandi157 – 161Combined sources5
Beta strandi164 – 172Combined sources9
Helixi173 – 189Combined sources17
Beta strandi194 – 199Combined sources6
Turni201 – 203Combined sources3
Helixi205 – 220Combined sources16
Beta strandi225 – 231Combined sources7
Helixi232 – 239Combined sources8
Helixi243 – 245Combined sources3
Beta strandi248 – 251Combined sources4
Helixi253 – 267Combined sources15
Helixi270 – 272Combined sources3
Beta strandi275 – 278Combined sources4
Helixi280 – 282Combined sources3
Beta strandi284 – 287Combined sources4
Helixi294 – 296Combined sources3
Turni297 – 300Combined sources4
Helixi305 – 318Combined sources14
Helixi321 – 337Combined sources17
Beta strandi338 – 340Combined sources3
Helixi343 – 345Combined sources3
Helixi351 – 363Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5GREX-ray2.65A28-366[»]
5GRFX-ray2.50A28-366[»]
5GRHX-ray2.80A28-366[»]
5GRIX-ray2.31A28-366[»]
5GRLX-ray2.79A28-366[»]
ProteinModelPortaliP50213.
SMRiP50213.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0785. Eukaryota.
COG0473. LUCA.
GeneTreeiENSGT00550000074918.
HOGENOMiHOG000021113.
HOVERGENiHBG052080.
InParanoidiP50213.
KOiK00030.
OMAiNQKQVTR.
OrthoDBiEOG091G094X.
PhylomeDBiP50213.
TreeFamiTF105692.

Family and domain databases

InterProiView protein in InterPro
IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
PfamiView protein in Pfam
PF00180. Iso_dh. 1 hit.
SMARTiView protein in SMART
SM01329. Iso_dh. 1 hit.
TIGRFAMsiTIGR00175. mito_nad_idh. 1 hit.
PROSITEiView protein in PROSITE
PS00470. IDH_IMDH. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P50213-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAGPAWISKV SRLLGAFHNP KQVTRGFTGG VQTVTLIPGD GIGPEISAAV
60 70 80 90 100
MKIFDAAKAP IQWEERNVTA IQGPGGKWMI PSEAKESMDK NKMGLKGPLK
110 120 130 140 150
TPIAAGHPSM NLLLRKTFDL YANVRPCVSI EGYKTPYTDV NIVTIRENTE
160 170 180 190 200
GEYSGIEHVI VDGVVQSIKL ITEGASKRIA EFAFEYARNN HRSNVTAVHK
210 220 230 240 250
ANIMRMSDGL FLQKCREVAE SCKDIKFNEM YLDTVCLNMV QDPSQFDVLV
260 270 280 290 300
MPNLYGDILS DLCAGLIGGL GVTPSGNIGA NGVAIFESVH GTAPDIAGKD
310 320 330 340 350
MANPTALLLS AVMMLRHMGL FDHAARIEAA CFATIKDGKS LTKDLGGNAK
360
CSDFTEEICR RVKDLD
Length:366
Mass (Da):39,592
Last modified:October 1, 1996 - v1
Checksum:i695F6A34F97430CF
GO
Isoform 2 (identifier: P50213-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-78: Missing.

Note: No experimental confirmation available.
Show »
Length:288
Mass (Da):31,381
Checksum:iBF8327BD4AA7D3EC
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0145161 – 78Missing in isoform 2. 1 PublicationAdd BLAST78

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U07681 mRNA. Translation: AAA85639.1.
AL442090 mRNA. Translation: CAC09449.1.
CH471136 Genomic DNA. Translation: EAW99181.1.
CH471136 Genomic DNA. Translation: EAW99182.1.
BC021967 mRNA. Translation: AAH21967.1.
CCDSiCCDS10297.1. [P50213-1]
PIRiS55282.
RefSeqiNP_005521.1. NM_005530.2. [P50213-1]
UniGeneiHs.591110.

Genome annotation databases

EnsembliENST00000299518; ENSP00000299518; ENSG00000166411. [P50213-1]
GeneIDi3419.
KEGGihsa:3419.
UCSCiuc002bdd.4. human. [P50213-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U07681 mRNA. Translation: AAA85639.1.
AL442090 mRNA. Translation: CAC09449.1.
CH471136 Genomic DNA. Translation: EAW99181.1.
CH471136 Genomic DNA. Translation: EAW99182.1.
BC021967 mRNA. Translation: AAH21967.1.
CCDSiCCDS10297.1. [P50213-1]
PIRiS55282.
RefSeqiNP_005521.1. NM_005530.2. [P50213-1]
UniGeneiHs.591110.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5GREX-ray2.65A28-366[»]
5GRFX-ray2.50A28-366[»]
5GRHX-ray2.80A28-366[»]
5GRIX-ray2.31A28-366[»]
5GRLX-ray2.79A28-366[»]
ProteinModelPortaliP50213.
SMRiP50213.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109645. 51 interactors.
IntActiP50213. 10 interactors.
MINTiMINT-1148360.
STRINGi9606.ENSP00000299518.

Chemistry databases

DrugBankiDB00157. NADH.

PTM databases

iPTMnetiP50213.
PhosphoSitePlusiP50213.
SwissPalmiP50213.

Polymorphism and mutation databases

BioMutaiIDH3A.
DMDMi1708399.

2D gel databases

OGPiP50213.
REPRODUCTION-2DPAGEiIPI00030702.

Proteomic databases

EPDiP50213.
MaxQBiP50213.
PaxDbiP50213.
PeptideAtlasiP50213.
PRIDEiP50213.

Protocols and materials databases

DNASUi3419.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000299518; ENSP00000299518; ENSG00000166411. [P50213-1]
GeneIDi3419.
KEGGihsa:3419.
UCSCiuc002bdd.4. human. [P50213-1]

Organism-specific databases

CTDi3419.
DisGeNETi3419.
GeneCardsiIDH3A.
HGNCiHGNC:5384. IDH3A.
HPAiHPA041465.
HPA062971.
MIMi601149. gene.
neXtProtiNX_P50213.
OpenTargetsiENSG00000166411.
PharmGKBiPA29632.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0785. Eukaryota.
COG0473. LUCA.
GeneTreeiENSGT00550000074918.
HOGENOMiHOG000021113.
HOVERGENiHBG052080.
InParanoidiP50213.
KOiK00030.
OMAiNQKQVTR.
OrthoDBiEOG091G094X.
PhylomeDBiP50213.
TreeFamiTF105692.

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000166411-MONOMER.
ReactomeiR-HSA-71403. Citric acid cycle (TCA cycle).
SABIO-RKiP50213.

Miscellaneous databases

ChiTaRSiIDH3A. human.
GeneWikiiIDH3A.
GenomeRNAii3419.
PROiPR:P50213.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000166411.
CleanExiHS_IDH3A.
ExpressionAtlasiP50213. baseline and differential.
GenevisibleiP50213. HS.

Family and domain databases

InterProiView protein in InterPro
IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
PfamiView protein in Pfam
PF00180. Iso_dh. 1 hit.
SMARTiView protein in SMART
SM01329. Iso_dh. 1 hit.
TIGRFAMsiTIGR00175. mito_nad_idh. 1 hit.
PROSITEiView protein in PROSITE
PS00470. IDH_IMDH. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiIDH3A_HUMAN
AccessioniPrimary (citable) accession number: P50213
Secondary accession number(s): D3DW83, Q9H3X0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: May 10, 2017
This is version 173 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.