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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: 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 sitei109SubstrateBy similarity1
Binding sitei140SubstrateBy similarity1
Sitei194Critical for catalysisBy similarity1
Metal bindingi228Magnesium or manganeseBy similarity1
Binding sitei228SubstrateBy similarity1

GO - Molecular functioni

GO - Biological processi

  • glutamate biosynthetic process Source: SGD
  • isocitrate metabolic process Source: SGD
  • protein targeting to mitochondrion Source: Reactome
  • 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:YNL037C-MONOMER.
YEAST:YNL037C-MONOMER.
BRENDAi1.1.1.41. 984.
ReactomeiR-SCE-1268020. Mitochondrial protein import.
R-SCE-71403. Citric acid cycle (TCA cycle).

Protein family/group databases

MoonProtiP28834.

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
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL037C.
SGDiS000004982. IDH1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • mitochondrial intermembrane space Source: Reactome
  • mitochondrial isocitrate dehydrogenase complex (NAD+) Source: SGD
  • mitochondrial matrix Source: SGD
  • mitochondrial nucleoid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 11Mitochondrion1 PublicationAdd BLAST11
ChainiPRO_000001443112 – 360Isocitrate dehydrogenase [NAD] subunit 1, mitochondrialAdd BLAST349

Proteomic databases

MaxQBiP28834.
PRIDEiP28834.

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. 142 interactors.
DIPiDIP-4376N.
IntActiP28834. 8 interactors.
MINTiMINT-484546.

Structurei

Secondary structure

1360
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi29 – 37Combined sources9
Helixi38 – 53Combined sources16
Beta strandi57 – 62Combined sources6
Helixi71 – 84Combined sources14
Beta strandi85 – 91Combined sources7
Helixi95 – 99Combined sources5
Helixi102 – 110Combined sources9
Beta strandi114 – 122Combined sources9
Beta strandi135 – 141Combined sources7
Helixi145 – 148Combined sources4
Beta strandi150 – 153Combined sources4
Beta strandi158 – 166Combined sources9
Helixi167 – 183Combined sources17
Beta strandi188 – 193Combined sources6
Turni195 – 197Combined sources3
Helixi201 – 216Combined sources16
Beta strandi220 – 226Combined sources7
Helixi227 – 236Combined sources10
Helixi238 – 240Combined sources3
Beta strandi242 – 246Combined sources5
Helixi248 – 262Combined sources15
Helixi265 – 267Combined sources3
Beta strandi269 – 276Combined sources8
Beta strandi278 – 280Combined sources3
Turni283 – 286Combined sources4
Helixi289 – 291Combined sources3
Helixi300 – 313Combined sources14
Helixi317 – 331Combined sources15
Beta strandi332 – 335Combined sources4
Helixi338 – 340Combined sources3
Helixi346 – 358Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28834.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

GeneTreeiENSGT00590000083091.
HOGENOMiHOG000021113.
InParanoidiP28834.
KOiK00030.
OMAiNSVRSAQ.
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.

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.
PIRiS31264.
RefSeqiNP_014361.1. NM_001182876.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35787. 142 interactors.
DIPiDIP-4376N.
IntActiP28834. 8 interactors.
MINTiMINT-484546.

Protein family/group databases

MoonProtiP28834.

Proteomic databases

MaxQBiP28834.
PRIDEiP28834.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YNL037C.
SGDiS000004982. IDH1.

Phylogenomic databases

GeneTreeiENSGT00590000083091.
HOGENOMiHOG000021113.
InParanoidiP28834.
KOiK00030.
OMAiNSVRSAQ.
OrthoDBiEOG092C2YAZ.

Enzyme and pathway databases

BioCyciMetaCyc:YNL037C-MONOMER.
YEAST:YNL037C-MONOMER.
BRENDAi1.1.1.41. 984.
ReactomeiR-SCE-1268020. Mitochondrial protein import.
R-SCE-71403. Citric acid cycle (TCA cycle).

Miscellaneous databases

EvolutionaryTraceiP28834.
PROiP28834.

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 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 2, 2016
This is version 147 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

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.