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P28834

- IDH1_YEAST

UniProt

P28834 - IDH1_YEAST

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Protein

Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial

Gene

IDH1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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 Mn(2+) 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 sitei109 – 1091SubstrateBy similarity
Binding sitei140 – 1401SubstrateBy similarity
Sitei194 – 1941Critical for catalysisBy similarity
Metal bindingi228 – 2281Magnesium or manganeseBy similarity
Binding sitei228 – 2281SubstrateBy similarity

GO - Molecular functioni

  1. isocitrate dehydrogenase (NAD+) activity Source: UniProtKB-EC
  2. magnesium ion binding Source: InterPro
  3. NAD binding Source: InterPro
  4. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. glutamate biosynthetic process Source: SGD
  2. isocitrate metabolic process Source: SGD
  3. 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-13685.
YEAST:YNL037C-MONOMER.
ReactomeiREACT_189012. Mitochondrial protein import.
REACT_245486. Citric acid cycle (TCA cycle).

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial (EC:1.1.1.41)
Alternative name(s):
Isocitric dehydrogenase
NAD(+)-specific ICDH
Gene namesi
Name:IDH1
Ordered Locus Names:YNL037C
ORF Names:N2690
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XIV

Organism-specific databases

CYGDiYNL037c.
SGDiS000004982. IDH1.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: Reactome
  2. mitochondrial intermembrane space Source: Reactome
  3. mitochondrial isocitrate dehydrogenase complex (NAD+) Source: SGD
  4. mitochondrial matrix Source: SGD
  5. mitochondrial nucleoid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 1111Mitochondrion1 PublicationAdd
BLAST
Chaini12 – 360349Isocitrate dehydrogenase [NAD] subunit 1, mitochondrialPRO_0000014431Add
BLAST

Proteomic databases

MaxQBiP28834.
PaxDbiP28834.
PeptideAtlasiP28834.

Expressioni

Gene expression databases

GenevestigatoriP28834.

Interactioni

Subunit structurei

Octamer of two non-identical subunits IDH1 and IDH2.

Binary interactionsi

WithEntry#Exp.IntActNotes
IDH2P282417EBI-8878,EBI-8883

Protein-protein interaction databases

BioGridi35787. 137 interactions.
DIPiDIP-4376N.
IntActiP28834. 6 interactions.
MINTiMINT-484546.
STRINGi4932.YNL037C.

Structurei

Secondary structure

1
360
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi29 – 379Combined sources
Helixi38 – 5316Combined sources
Beta strandi57 – 626Combined sources
Helixi71 – 8414Combined sources
Beta strandi85 – 917Combined sources
Helixi95 – 995Combined sources
Helixi102 – 1109Combined sources
Beta strandi114 – 1229Combined sources
Beta strandi135 – 1417Combined sources
Helixi145 – 1484Combined sources
Beta strandi150 – 1534Combined sources
Beta strandi158 – 1669Combined sources
Helixi167 – 18317Combined sources
Beta strandi188 – 1936Combined sources
Turni195 – 1973Combined sources
Helixi201 – 21616Combined sources
Beta strandi220 – 2267Combined sources
Helixi227 – 23610Combined sources
Helixi238 – 2403Combined sources
Beta strandi242 – 2465Combined sources
Helixi248 – 26215Combined sources
Helixi265 – 2673Combined sources
Beta strandi269 – 2768Combined sources
Beta strandi278 – 2803Combined sources
Turni283 – 2864Combined sources
Helixi289 – 2913Combined sources
Helixi300 – 31314Combined sources
Helixi317 – 33115Combined sources
Beta strandi332 – 3354Combined sources
Helixi338 – 3403Combined sources
Helixi346 – 35813Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BLVX-ray3.20A/C/E/G12-360[»]
3BLWX-ray4.30A/C/E/G/I/K/M/O12-360[»]
3BLXX-ray2.70A/C/E/G/I/K/M/O12-360[»]
ProteinModelPortaliP28834.
SMRiP28834. Positions 28-360.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28834.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0473.
GeneTreeiENSGT00590000083091.
HOGENOMiHOG000021113.
InParanoidiP28834.
KOiK00030.
OMAiMASCDAT.
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.

P28834-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLNRTIAKRT LATAAQAERT LPKKYGGRFT VTLIPGDGVG KEITDSVRTI
60 70 80 90 100
FEAENIPIDW ETINIKQTDH KEGVYEAVES LKRNKIGLKG LWHTPADQTG
110 120 130 140 150
HGSLNVALRK QLDIYANVAL FKSLKGVKTR IPDIDLIVIR ENTEGEFSGL
160 170 180 190 200
EHESVPGVVE SLKVMTRPKT ERIARFAFDF AKKYNRKSVT AVHKANIMKL
210 220 230 240 250
GDGLFRNIIT EIGQKEYPDI DVSSIIVDNA SMQAVAKPHQ FDVLVTPSMY
260 270 280 290 300
GTILGNIGAA LIGGPGLVAG ANFGRDYAVF EPGSRHVGLD IKGQNVANPT
310 320 330 340 350
AMILSSTLML NHLGLNEYAT RISKAVHETI AEGKHTTRDI GGSSSTTDFT
360
NEIINKLSTM
Length:360
Mass (Da):39,324
Last modified:July 1, 1993 - v2
Checksum:i0932E7B3CD685240
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95203 Genomic DNA. Translation: AAA34711.1.
Z71313 Genomic DNA. Translation: CAA95904.1.
BK006947 Genomic DNA. Translation: DAA10508.1.
PIRiS31264.
RefSeqiNP_014361.1. NM_001182876.1.

Genome annotation databases

EnsemblFungiiYNL037C; YNL037C; YNL037C.
GeneIDi855691.
KEGGisce:YNL037C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95203 Genomic DNA. Translation: AAA34711.1 .
Z71313 Genomic DNA. Translation: CAA95904.1 .
BK006947 Genomic DNA. Translation: DAA10508.1 .
PIRi S31264.
RefSeqi NP_014361.1. NM_001182876.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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 [» ]
ProteinModelPortali P28834.
SMRi P28834. Positions 28-360.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 35787. 137 interactions.
DIPi DIP-4376N.
IntActi P28834. 6 interactions.
MINTi MINT-484546.
STRINGi 4932.YNL037C.

Proteomic databases

MaxQBi P28834.
PaxDbi P28834.
PeptideAtlasi P28834.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YNL037C ; YNL037C ; YNL037C .
GeneIDi 855691.
KEGGi sce:YNL037C.

Organism-specific databases

CYGDi YNL037c.
SGDi S000004982. IDH1.

Phylogenomic databases

eggNOGi COG0473.
GeneTreei ENSGT00590000083091.
HOGENOMi HOG000021113.
InParanoidi P28834.
KOi K00030.
OMAi MASCDAT.
OrthoDBi EOG75XGWZ.

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-13685.
YEAST:YNL037C-MONOMER.
Reactomei REACT_189012. Mitochondrial protein import.
REACT_245486. Citric acid cycle (TCA cycle).

Miscellaneous databases

EvolutionaryTracei P28834.
NextBioi 980007.
PROi P28834.

Gene expression databases

Genevestigatori P28834.

Family and domain databases

Gene3Di 3.40.718.10. 1 hit.
InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view ]
PANTHERi PTHR11835. PTHR11835. 1 hit.
Pfami PF00180. Iso_dh. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR00175. mito_nad_idh. 1 hit.
PROSITEi PS00470. IDH_IMDH. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "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 12-27.
    Strain: SG7.
  5. "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.
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiIDH1_YEAST
AccessioniPrimary (citable) accession number: P28834
Secondary accession number(s): D6W1E2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: July 1, 1993
Last modified: November 26, 2014
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 10500 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

External Data

Dasty 3