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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 Mg(2+) or Mn2+ ion per subunit.By similarity

Enzyme regulationi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei119 – 1191SubstrateBy similarity
Binding sitei129 – 1291SubstrateBy similarity
Binding sitei150 – 1501SubstrateBy similarity
Sitei157 – 1571Critical for catalysisBy similarity
Sitei204 – 2041Critical for catalysisBy similarity
Metal bindingi237 – 2371Magnesium or manganeseBy similarity
Binding sitei237 – 2371SubstrateBy similarity
Metal bindingi263 – 2631Magnesium or manganeseBy similarity
Metal bindingi267 – 2671Magnesium or manganeseBy similarity

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:MONOMER-13686.
YEAST:YOR136W-MONOMER.
BRENDAi1.1.1.41. 984.
ReactomeiREACT_278278. 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
ProteomesiUP000002311 Componenti: Chromosome XV

Organism-specific databases

CYGDiYOR136w.
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)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 1515Mitochondrion2 PublicationsAdd
BLAST
Chaini16 – 369354Isocitrate dehydrogenase [NAD] subunit 2, mitochondrialPRO_0000014434Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei105 – 1051Phosphothreonine1 Publication
Modified residuei153 – 1531Phosphothreonine2 Publications
Modified residuei327 – 3271Phosphothreonine1 Publication
Modified residuei349 – 3491Phosphothreonine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP28241.
PaxDbiP28241.
PeptideAtlasiP28241.

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. 173 interactions.
DIPiDIP-4296N.
IntActiP28241. 26 interactions.
MINTiMINT-559185.
STRINGi4932.YOR136W.

Structurei

Secondary structure

1
369
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi22 – 243Combined sources
Turni32 – 343Combined sources
Helixi48 – 6013Combined sources
Turni61 – 633Combined sources
Beta strandi65 – 673Combined sources
Beta strandi76 – 783Combined sources
Beta strandi81 – 833Combined sources
Helixi86 – 9510Combined sources
Beta strandi96 – 1005Combined sources
Helixi114 – 1229Combined sources
Beta strandi124 – 1329Combined sources
Beta strandi145 – 1517Combined sources
Beta strandi153 – 16311Combined sources
Beta strandi168 – 1769Combined sources
Helixi177 – 19317Combined sources
Beta strandi197 – 2048Combined sources
Turni206 – 2083Combined sources
Helixi210 – 22314Combined sources
Beta strandi229 – 2357Combined sources
Helixi236 – 24510Combined sources
Helixi247 – 2504Combined sources
Beta strandi253 – 2575Combined sources
Helixi259 – 27315Combined sources
Helixi277 – 2793Combined sources
Beta strandi281 – 2888Combined sources
Beta strandi290 – 2945Combined sources
Helixi300 – 3023Combined sources
Turni303 – 3064Combined sources
Helixi311 – 32414Combined sources
Helixi327 – 3359Combined sources
Helixi337 – 3415Combined sources
Helixi350 – 3523Combined sources
Helixi358 – 36710Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 19-369.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28241.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0473.
GeneTreeiENSGT00550000074918.
HOGENOMiHOG000021113.
InParanoidiP28241.
KOiK00030.
OMAiQITTFAY.
OrthoDBiEOG75XGWZ.

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]
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti25 – 251R → G AA sequence (PubMed:2198251).Curated

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
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. Positions 19-369.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34531. 173 interactions.
DIPiDIP-4296N.
IntActiP28241. 26 interactions.
MINTiMINT-559185.
STRINGi4932.YOR136W.

Protein family/group databases

MoonProtiP28241.

Proteomic databases

MaxQBiP28241.
PaxDbiP28241.
PeptideAtlasiP28241.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CYGDiYOR136w.
EuPathDBiFungiDB:YOR136W.
SGDiS000005662. IDH2.

Phylogenomic databases

eggNOGiCOG0473.
GeneTreeiENSGT00550000074918.
HOGENOMiHOG000021113.
InParanoidiP28241.
KOiK00030.
OMAiQITTFAY.
OrthoDBiEOG75XGWZ.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13686.
YEAST:YOR136W-MONOMER.
BRENDAi1.1.1.41. 984.
ReactomeiREACT_278278. Citric acid cycle (TCA cycle).

Miscellaneous databases

EvolutionaryTraceiP28241.
NextBioi976313.
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]
TIGRFAMsiTIGR00175. mito_nad_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "NAD(+)-dependent isocitrate dehydrogenase. Cloning, nucleotide sequence, and disruption of the IDH2 gene from Saccharomyces cerevisiae."
    Cupp J.R., McAlister-Henn L.
    J. Biol. Chem. 266:22199-22205(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequencing and analysis of 51 kb on the right arm of chromosome XV from Saccharomyces cerevisiae reveals 30 open reading frames."
    Wiemann S., Rechmann S., Benes V., Voss H., Schwager C., Vlcek C., Stegemann J., Zimmermann J., Erfle H., Paces V., Ansorge W.
    Yeast 12:281-288(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "Subunit structure, expression, and function of NAD(H)-specific isocitrate dehydrogenase in Saccharomyces cerevisiae."
    Keys D.A., McAlister-Henn L.
    J. Bacteriol. 172:4280-4287(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 16-26.
    Strain: SG7.
  7. "Yeast mitochondrial NAD(+)-dependent isocitrate dehydrogenase is an RNA-binding protein."
    Elzinga S.D.J., Bednarz A.L., van Oosterum K., Dekker P.J.T., Grivell L.A.
    Nucleic Acids Res. 21:5328-5331(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: RNA-BINDING, PROTEIN SEQUENCE OF 16-34.
  8. "Yeast mitochondrial dehydrogenases are associated in a supramolecular complex."
    Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S., Schmitter J.-M.
    Biochemistry 40:9758-9769(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase."
    Reinders J., Wagner K., Zahedi R.P., Stojanovski D., Eyrich B., van der Laan M., Rehling P., Sickmann A., Pfanner N., Meisinger C.
    Mol. Cell. Proteomics 6:1896-1906(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-349, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ATCC 76625 / YPH499.
  11. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-105 AND THR-153, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-153 AND THR-327, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

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: June 24, 2015
This is version 144 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

External Data

Dasty 3

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 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.