Reviewed, UniProtKB/Swiss-Prot P28834 (IDH1_YEAST)

Names and origin

Protein names

Recommended name:
    Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial
    EC=1.1.1.41
Alternative name(s):
    Isocitric dehydrogenase
    NAD(+)-specific ICDH

Gene names

Name:	IDH1
Ordered Locus Names:	YNL037C
ORF Names:	N2690

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	360 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.
Miscellaneous	Present with 10500 molecules/cell in log phase SD medium. Ref.5
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
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 mitochondrial nucleoid 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
IDH2	P28241	2	EBI-8878,EBI-8883

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 11

11

Mitochondrion Ref.3

Chain

12 – 360

349

Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial

PRO_0000014431

Sites

Metal binding

228

1

Magnesium or manganese By similarity

Binding site

109

1

Substrate By similarity

Binding site

140

1

Substrate By similarity

Binding site

228

1

Substrate By similarity

Site

194

1

Critical for catalysis By similarity

Secondary structure

1

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360

Helix Strand Turn

Details...

Beta strand

29 – 34

6

Turn

37 – 39

3

Helix

40 – 52

13

Turn

53 – 55

3

Beta strand

57 – 62

6

Helix

74 – 84

11

Beta strand

85 – 89

5

Helix

106 – 112

7

Beta strand

116 – 122

7

Beta strand

135 – 155

21

Beta strand

158 – 166

9

Helix

167 – 183

17

Beta strand

188 – 193

6

Turn

195 – 197

3

Helix

201 – 211

11

Turn

212 – 214

3

Beta strand

220 – 226

7

Helix

227 – 236

10

Helix

238 – 240

3

Beta strand

242 – 246

5

Helix

248 – 261

14

Beta strand

269 – 273

5

Beta strand

278 – 284

7

Helix

289 – 291

3

Helix

300 – 312

13

Helix

317 – 331

15

Beta strand

332 – 335

4

Helix

338 – 340

3

Helix

346 – 357

12

Sequences

	Sequence		Length	Mass (Da)
	P28834-1 [UniParc]. Last modified July 1, 1993. Version 2. Checksum: 0932E7B3CD685240	FASTA	360	39,324
	10 20 30 40 50 60 MLNRTIAKRT LATAAQAERT LPKKYGGRFT VTLIPGDGVG KEITDSVRTI FEAENIPIDW 70 80 90 100 110 120 ETINIKQTDH KEGVYEAVES LKRNKIGLKG LWHTPADQTG HGSLNVALRK QLDIYANVAL 130 140 150 160 170 180 FKSLKGVKTR IPDIDLIVIR ENTEGEFSGL EHESVPGVVE SLKVMTRPKT ERIARFAFDF 190 200 210 220 230 240 AKKYNRKSVT AVHKANIMKL GDGLFRNIIT EIGQKEYPDI DVSSIIVDNA SMQAVAKPHQ 250 260 270 280 290 300 FDVLVTPSMY GTILGNIGAA LIGGPGLVAG ANFGRDYAVF EPGSRHVGLD IKGQNVANPT 310 320 330 340 350 360 AMILSSTLML NHLGLNEYAT RISKAVHETI AEGKHTTRDI GGSSSTTDFT NEIINKLSTM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of the gene encoding the IDH1 subunit of NAD(+)-dependent isocitrate dehydrogenase from Saccharomyces cerevisiae." Cupp J.R., McAlister-Henn L. J. Biol. Chem. 267:16417-16423(1992) [PubMed: 1644826] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 49-61; 72-83; 325-333 AND 339-356.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed: 9169873] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"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 12-27. Strain: SG7.
[4]	"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.
[5]	"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].
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M95203 Genomic DNA. Translation: AAA34711.1.
Z71313 Genomic DNA. Translation: CAA95904.1.

PIR

S31264.

RefSeq

NP_014361.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3BLV	X-ray	3.20	A/C/E/G	12-360	[»]
3BLW	X-ray	4.30	A/C/E/G/I/K/M/O	12-360	[»]
3BLX	X-ray	2.70	A/C/E/G/I/K/M/O	12-360	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:4376N.

IntAct

P28834. 15 interactions.

Proteomic databases

PeptideAtlas

P28834.

PRIDE

P28834.

Genome annotation databases

Ensembl

YNL037C. Saccharomyces cerevisiae. [Contig view]

GeneID

855691.

GenomeReviews

Gene locus YNL037C in contig Y13139_GR.

KEGG

sce:YNL037C.

NMPDR

fig|4932.3.peg.5438.

Organism-specific databases

CYGD

YNL037c.

SGD

S000004982. IDH1.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P28834.

OMA

P28834. NVALRKQ.

Enzyme and pathway databases

BioCyc

MetaCyc:MON-13685.

BRENDA

1.1.1.41. 250.

Gene expression databases

ArrayExpress

P28834.

GermOnline

YNL037C. 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

980007.

Entry information

Entry name

IDH1_YEAST

Accession

Primary (citable) accession number: P28834

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	July 1, 1993
Last modified:	June 16, 2009
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)