Reviewed, UniProtKB/Swiss-Prot P28241 (IDH2_YEAST)

Names and origin

Protein names

Recommended name:
    Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial
    EC=1.1.1.41
Alternative name(s):
    Isocitric dehydrogenase
    NAD(+)-specific ICDH

Gene names

Name:	IDH2
Ordered Locus Names:	YOR136W
ORF Names:	O3326, YOR3326W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	369 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 activity	Isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH.
Cofactor	Binds 1 magnesium or manganese ion per subunit By similarity.
Enzyme regulation	Allosterically regulated by several compounds including AMP, NAD+, and citrate.
Subunit structure	Octamer of two non-identical subunits IDH1 and IDH2.
Subcellular location	Mitochondrion matrix. Ref.7
Miscellaneous	Present with 43100 molecules/cell in log phase SD medium. Ref.8
Sequence similarities	Belongs to the isocitrate and isopropylmalate dehydrogenases family.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	Magnesium Manganese Metal-binding NAD RNA-binding
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	3D-structure Allosteric enzyme Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	glutamate biosynthetic process Traceable author statement. Source: SGD isocitrate metabolic process Traceable author statement. Source: SGD oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW tricarboxylic acid cycle Traceable author statement. Source: SGD
Cellular component	mitochondrial isocitrate dehydrogenase complex (NAD+) Inferred from direct assay. Source: SGD
Molecular function	NAD or NADH binding Inferred from electronic annotation. Source: InterPro RNA binding Inferred from electronic annotation. Source: UniProtKB-KW isocitrate dehydrogenase (NAD+) activity Inferred from electronic annotation. Source: EC magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
IDH1	P28834	2	EBI-8883,EBI-8878

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 15

15

Mitochondrion Ref.5 Ref.6

Chain

16 – 369

354

Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial

PRO_0000014434

Sites

Metal binding

237

1

Magnesium or manganese By similarity

Metal binding

263

1

Magnesium or manganese By similarity

Metal binding

267

1

Magnesium or manganese By similarity

Binding site

119

1

Substrate By similarity

Binding site

129

1

Substrate By similarity

Binding site

150

1

Substrate By similarity

Binding site

237

1

Substrate By similarity

Site

157

1

Critical for catalysis By similarity

Site

204

1

Critical for catalysis By similarity

Amino acid modifications

Modified residue

105

1

Phosphothreonine Ref.10

Modified residue

153

1

Phosphothreonine Ref.10

Modified residue

349

1

Phosphothreonine Ref.9

Modified residue

360

1

Phosphoserine Ref.10

Experimental info

Sequence conflict

25

1

R → G AA sequence Ref.5

Secondary structure

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369

Helix Strand Turn

Details...

Helix

22 – 24

3

Beta strand

34 – 40

7

Helix

48 – 61

14

Beta strand

65 – 68

4

Helix

78 – 80

3

Helix

86 – 94

9

Beta strand

98 – 100

3

Helix

114 – 120

7

Turn

121 – 123

3

Beta strand

124 – 132

9

Beta strand

145 – 151

7

Beta strand

153 – 155

3

Beta strand

161 – 165

5

Beta strand

168 – 176

9

Helix

177 – 193

17

Beta strand

198 – 203

6

Turn

205 – 207

3

Helix

209 – 223

15

Beta strand

229 – 235

7

Helix

236 – 245

10

Helix

247 – 250

4

Beta strand

255 – 257

3

Helix

259 – 274

16

Beta strand

275 – 277

3

Beta strand

281 – 288

8

Beta strand

290 – 294

5

Turn

303 – 306

4

Helix

311 – 324

14

Helix

327 – 335

9

Helix

337 – 339

3

Turn

340 – 342

3

Helix

350 – 352

3

Helix

358 – 367

10

Sequences

	Sequence		Length	Mass (Da)
	P28241-1 [UniParc]. Last modified December 1, 1992. Version 1. Checksum: 3A48C999776CE373	FASTA	369	39,739
	10 20 30 40 50 60 MLRNTFFRNT SRRFLATVKQ PSIGRYTGKP NPSTGKYTVS FIEGDGIGPE ISKSVKKIFS 70 80 90 100 110 120 AANVPIEWES CDVSPIFVNG LTTIPDPAVQ SITKNLVALK GPLATPIGKG HRSLNLTLRK 130 140 150 160 170 180 TFGLFANVRP AKSIEGFKTT YENVDLVLIR ENTEGEYSGI EHIVCPGVVQ SIKLITRDAS 190 200 210 220 230 240 ERVIRYAFEY ARAIGRPRVI VVHKSTIQRL ADGLFVNVAK ELSKEYPDLT LETELIDNSV 250 260 270 280 290 300 LKVVTNPSAY TDAVSVCPNL YGDILSDLNS GLSAGSLGLT PSANIGHKIS IFEAVHGSAP 310 320 330 340 350 360 DIAGQDKANP TALLLSSVMM LNHMGLTNHA DQIQNAVLST IASGPENRTG DLAGTATTSS FTEAVIKRL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 1939242] [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: 8904341] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"DNA sequencing and analysis of 130 kb from yeast chromosome XV." Voss H., Benes V., Andrade M.A., Valencia A., Rechmann S., Teodoru C., Schwager C., Paces V., Sander C., Ansorge W. Yeast 13:655-672(1997) [PubMed: 9200815] [Abstract] 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: 9169874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	"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: 2198251] [Abstract] Cited for: PROTEIN SEQUENCE OF 16-26. Strain: SG7.
[6]	"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: 7505425] [Abstract] Cited for: RNA-BINDING, PROTEIN SEQUENCE OF 16-34.
[7]	"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: 11502169] [Abstract] Cited for: SUBCELLULAR LOCATION.
[8]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"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: 17761666] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-349, MASS SPECTROMETRY.
[10]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-105; THR-153 AND SER-360, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M74131 Genomic DNA. Translation: AAA34702.1.
X94335 Genomic DNA. Translation: CAA64054.1.
Z75043 Genomic DNA. Translation: CAA99335.1.
X90518 Genomic DNA. Translation: CAA62110.1.

PIR

A39309.

RefSeq

NP_014779.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3BLV	X-ray	3.20	B/D/F/H	16-369	[»]
3BLW	X-ray	4.30	B/D/F/H/J/L/N/P	16-369	[»]
3BLX	X-ray	2.70	B/D/F/H/J/L/N/P	16-369	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:4296N.

IntAct

P28241. 44 interactions.

Proteomic databases

PeptideAtlas

P28241.

PRIDE

P28241.

Genome annotation databases

Ensembl

YOR136W. Saccharomyces cerevisiae. [Contig view]

GeneID

854303.

GenomeReviews

Gene locus YOR136W in contig Y13140_GR.

KEGG

sce:YOR136W.

NMPDR

fig|4932.3.peg.5882.

Organism-specific databases

CYGD

YOR136w.

SGD

S000005662. IDH2.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P28241.

OMA

P28241. GGNSKCS.

Enzyme and pathway databases

BioCyc

MetaCyc:MON-13686.

BRENDA

1.1.1.41. 250.

Gene expression databases

GermOnline

YOR136W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004434. Isocitrate_DH_NAD_mit.
[Graphical view]

Gene3D

G3DSA:3.40.718.10. IDH_IMDH. 1 hit.

PANTHER

PTHR11835. IDH_IMDH_dimeric. 1 hit.

Pfam

PF00180. Iso_dh. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00175. mito_nad_idh. 1 hit.

PROSITE

PS00470. IDH_IMDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

976313.

Entry information

Entry name

IDH2_YEAST

Accession

Primary (citable) accession number: P28241

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	December 1, 1992
Last modified:	June 16, 2009
This is version 87 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)