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Protein

Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial

Gene

IDH2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs.

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

Enzyme regulationi

Allosterically regulated by several compounds including AMP, NAD+, and citrate.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei119SubstrateBy similarity1
Binding sitei129SubstrateBy similarity1
Binding sitei150SubstrateBy similarity1
Sitei157Critical for catalysisBy similarity1
Sitei204Critical for catalysisBy similarity1
Metal bindingi237Magnesium or manganeseBy similarity1
Binding sitei237SubstrateBy similarity1
Metal bindingi263Magnesium or manganeseBy similarity1
Metal bindingi267Magnesium or manganeseBy similarity1

GO - Molecular functioni

GO - Biological processi

  • glutamate biosynthetic process Source: SGD
  • isocitrate metabolic process Source: SGD
  • tricarboxylic acid cycle Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD, RNA-binding

Enzyme and pathway databases

BioCyciMetaCyc:YOR136W-MONOMER.
YEAST:YOR136W-MONOMER.
BRENDAi1.1.1.41. 984.
ReactomeiR-SCE-71403. Citric acid cycle (TCA cycle).

Protein family/group databases

MoonProtiP28241.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial (EC:1.1.1.41)
Alternative name(s):
Isocitric dehydrogenase
NAD(+)-specific ICDH
Gene namesi
Name:IDH2
Ordered Locus Names:YOR136W
ORF Names:O3326, YOR3326W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR136W.
SGDiS000005662. IDH2.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial isocitrate dehydrogenase complex (NAD+) Source: SGD
  • mitochondrion Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 15Mitochondrion2 PublicationsAdd BLAST15
ChainiPRO_000001443416 – 369Isocitrate dehydrogenase [NAD] subunit 2, mitochondrialAdd BLAST354

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei105PhosphothreonineCombined sources1
Modified residuei153PhosphothreonineCombined sources1
Modified residuei327PhosphothreonineCombined sources1
Modified residuei349PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP28241.
PRIDEiP28241.

PTM databases

iPTMnetiP28241.

Interactioni

Subunit structurei

Octamer of two non-identical subunits IDH1 and IDH2.

Binary interactionsi

WithEntry#Exp.IntActNotes
IDH1P288347EBI-8883,EBI-8878

Protein-protein interaction databases

BioGridi34531. 177 interactors.
DIPiDIP-4296N.
IntActiP28241. 27 interactors.
MINTiMINT-559185.

Structurei

Secondary structure

1369
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi22 – 24Combined sources3
Turni32 – 34Combined sources3
Helixi48 – 60Combined sources13
Turni61 – 63Combined sources3
Beta strandi65 – 67Combined sources3
Beta strandi76 – 78Combined sources3
Beta strandi81 – 83Combined sources3
Helixi86 – 95Combined sources10
Beta strandi96 – 100Combined sources5
Helixi114 – 122Combined sources9
Beta strandi124 – 132Combined sources9
Beta strandi145 – 151Combined sources7
Beta strandi153 – 163Combined sources11
Beta strandi168 – 176Combined sources9
Helixi177 – 193Combined sources17
Beta strandi197 – 204Combined sources8
Turni206 – 208Combined sources3
Helixi210 – 223Combined sources14
Beta strandi229 – 235Combined sources7
Helixi236 – 245Combined sources10
Helixi247 – 250Combined sources4
Beta strandi253 – 257Combined sources5
Helixi259 – 273Combined sources15
Helixi277 – 279Combined sources3
Beta strandi281 – 288Combined sources8
Beta strandi290 – 294Combined sources5
Helixi300 – 302Combined sources3
Turni303 – 306Combined sources4
Helixi311 – 324Combined sources14
Helixi327 – 335Combined sources9
Helixi337 – 341Combined sources5
Helixi350 – 352Combined sources3
Helixi358 – 367Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BLVX-ray3.20B/D/F/H16-369[»]
3BLWX-ray4.30B/D/F/H/J/L/N/P16-369[»]
3BLXX-ray2.70B/D/F/H/J/L/N/P16-369[»]
ProteinModelPortaliP28241.
SMRiP28241.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28241.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

GeneTreeiENSGT00550000074918.
HOGENOMiHOG000021113.
InParanoidiP28241.
KOiK00030.
OMAiNQKQVTR.
OrthoDBiEOG092C2YAZ.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00175. mito_nad_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P28241-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRNTFFRNT SRRFLATVKQ PSIGRYTGKP NPSTGKYTVS FIEGDGIGPE
60 70 80 90 100
ISKSVKKIFS AANVPIEWES CDVSPIFVNG LTTIPDPAVQ SITKNLVALK
110 120 130 140 150
GPLATPIGKG HRSLNLTLRK TFGLFANVRP AKSIEGFKTT YENVDLVLIR
160 170 180 190 200
ENTEGEYSGI EHIVCPGVVQ SIKLITRDAS ERVIRYAFEY ARAIGRPRVI
210 220 230 240 250
VVHKSTIQRL ADGLFVNVAK ELSKEYPDLT LETELIDNSV LKVVTNPSAY
260 270 280 290 300
TDAVSVCPNL YGDILSDLNS GLSAGSLGLT PSANIGHKIS IFEAVHGSAP
310 320 330 340 350
DIAGQDKANP TALLLSSVMM LNHMGLTNHA DQIQNAVLST IASGPENRTG
360
DLAGTATTSS FTEAVIKRL
Length:369
Mass (Da):39,739
Last modified:December 1, 1992 - v1
Checksum:i3A48C999776CE373
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25R → G AA sequence (PubMed:2198251).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M74131 Genomic DNA. Translation: AAA34702.1.
X94335 Genomic DNA. Translation: CAA64054.1.
Z75043 Genomic DNA. Translation: CAA99335.1.
X90518 Genomic DNA. Translation: CAA62110.1.
BK006948 Genomic DNA. Translation: DAA10909.1.
PIRiA39309.
RefSeqiNP_014779.1. NM_001183555.1.

Genome annotation databases

EnsemblFungiiYOR136W; YOR136W; YOR136W.
GeneIDi854303.
KEGGisce:YOR136W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M74131 Genomic DNA. Translation: AAA34702.1.
X94335 Genomic DNA. Translation: CAA64054.1.
Z75043 Genomic DNA. Translation: CAA99335.1.
X90518 Genomic DNA. Translation: CAA62110.1.
BK006948 Genomic DNA. Translation: DAA10909.1.
PIRiA39309.
RefSeqiNP_014779.1. NM_001183555.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BLVX-ray3.20B/D/F/H16-369[»]
3BLWX-ray4.30B/D/F/H/J/L/N/P16-369[»]
3BLXX-ray2.70B/D/F/H/J/L/N/P16-369[»]
ProteinModelPortaliP28241.
SMRiP28241.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34531. 177 interactors.
DIPiDIP-4296N.
IntActiP28241. 27 interactors.
MINTiMINT-559185.

Protein family/group databases

MoonProtiP28241.

PTM databases

iPTMnetiP28241.

Proteomic databases

MaxQBiP28241.
PRIDEiP28241.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR136W; YOR136W; YOR136W.
GeneIDi854303.
KEGGisce:YOR136W.

Organism-specific databases

EuPathDBiFungiDB:YOR136W.
SGDiS000005662. IDH2.

Phylogenomic databases

GeneTreeiENSGT00550000074918.
HOGENOMiHOG000021113.
InParanoidiP28241.
KOiK00030.
OMAiNQKQVTR.
OrthoDBiEOG092C2YAZ.

Enzyme and pathway databases

BioCyciMetaCyc:YOR136W-MONOMER.
YEAST:YOR136W-MONOMER.
BRENDAi1.1.1.41. 984.
ReactomeiR-SCE-71403. Citric acid cycle (TCA cycle).

Miscellaneous databases

EvolutionaryTraceiP28241.
PROiP28241.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00175. mito_nad_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiIDH2_YEAST
AccessioniPrimary (citable) accession number: P28241
Secondary accession number(s): D6W2J3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: November 2, 2016
This is version 157 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 43100 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

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.