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Protein

Isocitrate dehydrogenase [NADP], mitochondrial

Gene

IDP1

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

Mitochondrial IDP1 may regulate flux through the tricarboxylic acid cycle and respiration. Its probably critical function is the production of NADPH.

Catalytic activityi

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

Enzyme regulationi

The enzyme is subject to end product inhibition by NADPH and 2-oxoglutarate.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei93SubstrateBy similarity1
Binding sitei98NADPBy similarity1
Binding sitei125SubstrateBy similarity1
Binding sitei148SubstrateBy similarity1
Sitei155Critical for catalysisBy similarity1
Sitei229Critical for catalysisBy similarity1
Metal bindingi269Magnesium or manganeseBy similarity1
Binding sitei277NADPBy similarity1
Metal bindingi292Magnesium or manganeseBy similarity1
Binding sitei345NADP; via amide nitrogen and carbonyl oxygenBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi91 – 93NADPBy similarity3
Nucleotide bindingi327 – 332NADPBy similarity6

GO - Molecular functioni

  • isocitrate dehydrogenase (NADP+) activity Source: SGD
  • magnesium ion binding Source: InterPro
  • NAD binding Source: InterPro

GO - Biological processi

  • glutamate biosynthetic process Source: SGD
  • glyoxylate cycle Source: UniProtKB-KW
  • isocitrate metabolic process Source: InterPro
  • tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyciYEAST:YDL066W-MONOMER.
BRENDAi1.1.1.42. 984.
SABIO-RKP21954.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP], mitochondrial (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:IDP1
Ordered Locus Names:YDL066W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL066W.
SGDiS000002224. IDP1.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial nucleoid Source: SGD
  • mitochondrion Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 16Mitochondrion1 PublicationAdd BLAST16
ChainiPRO_000001442617 – 428Isocitrate dehydrogenase [NADP], mitochondrialAdd BLAST412

Proteomic databases

MaxQBiP21954.
PRIDEiP21954.

Expressioni

Inductioni

By growth with glucose as a carbon source.

Interactioni

Subunit structurei

Homodimer.

Binary interactionsi

WithEntry#Exp.IntActNotes
KAR2P164742EBI-8898,EBI-7876

Protein-protein interaction databases

BioGridi31993. 46 interactors.
DIPiDIP-4494N.
IntActiP21954. 19 interactors.
MINTiMINT-510681.

Structurei

Secondary structure

1428
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi26 – 30Combined sources5
Helixi33 – 46Combined sources14
Turni47 – 50Combined sources4
Beta strandi55 – 59Combined sources5
Helixi62 – 67Combined sources6
Turni68 – 70Combined sources3
Helixi71 – 83Combined sources13
Beta strandi84 – 88Combined sources5
Helixi96 – 101Combined sources6
Helixi111 – 119Combined sources9
Beta strandi121 – 127Combined sources7
Beta strandi142 – 149Combined sources8
Helixi153 – 156Combined sources4
Beta strandi158 – 162Combined sources5
Beta strandi164 – 175Combined sources12
Turni177 – 179Combined sources3
Beta strandi183 – 192Combined sources10
Beta strandi194 – 202Combined sources9
Helixi203 – 220Combined sources18
Beta strandi224 – 228Combined sources5
Turni230 – 232Combined sources3
Helixi236 – 251Combined sources16
Helixi253 – 259Combined sources7
Beta strandi263 – 267Combined sources5
Helixi268 – 277Combined sources10
Beta strandi280 – 286Combined sources7
Helixi288 – 302Combined sources15
Beta strandi307 – 313Combined sources7
Beta strandi315 – 318Combined sources4
Beta strandi320 – 323Combined sources4
Helixi330 – 337Combined sources8
Helixi347 – 364Combined sources18
Helixi367 – 385Combined sources19
Helixi392 – 397Combined sources6
Helixi403 – 405Combined sources3
Helixi409 – 426Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2QFVX-ray2.30A/B/C/D16-428[»]
2QFWX-ray2.60A/B/C/D/E/F16-428[»]
2QFXX-ray2.70A/B/C/D/E/F16-428[»]
2QFYX-ray2.10A/B/C/D/E/F16-428[»]
ProteinModelPortaliP21954.
SMRiP21954.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21954.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni110 – 116Substrate bindingBy similarity7

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
InParanoidiP21954.
KOiK00031.
OMAiPENGEPQ.
OrthoDBiEOG092C2D51.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004790. Isocitrate_DH_NADP.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11822. PTHR11822. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000108. IDH_NADP. 1 hit.
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00127. nadp_idh_euk. 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.

P21954-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSMLSRRLFS TSRLAAFSKI KVKQPVVELD GDEMTRIIWD KIKKKLILPY
60 70 80 90 100
LDVDLKYYDL SVESRDATSD KITQDAAEAI KKYGVGIKCA TITPDEARVK
110 120 130 140 150
EFNLHKMWKS PNGTIRNILG GTVFREPIVI PRIPRLVPRW EKPIIIGRHA
160 170 180 190 200
HGDQYKATDT LIPGPGSLEL VYKPSDPTTA QPQTLKVYDY KGSGVAMAMY
210 220 230 240 250
NTDESIEGFA HSSFKLAIDK KLNLFLSTKN TILKKYDGRF KDIFQEVYEA
260 270 280 290 300
QYKSKFEQLG IHYEHRLIDD MVAQMIKSKG GFIMALKNYD GDVQSDIVAQ
310 320 330 340 350
GFGSLGLMTS ILVTPDGKTF ESEAAHGTVT RHYRKYQKGE ETSTNSIASI
360 370 380 390 400
FAWSRGLLKR GELDNTPALC KFANILESAT LNTVQQDGIM TKDLALACGN
410 420
NERSAYVTTE EFLDAVEKRL QKEIKSIE
Length:428
Mass (Da):48,190
Last modified:August 1, 1991 - v1
Checksum:i7F885785B8682416
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57229 Genomic DNA. Translation: AAA34703.1.
Z74114 Genomic DNA. Translation: CAA98631.1.
BK006938 Genomic DNA. Translation: DAA11791.1.
PIRiA38610. DCBYIS.
RefSeqiNP_010217.1. NM_001180125.1.

Genome annotation databases

EnsemblFungiiYDL066W; YDL066W; YDL066W.
GeneIDi851493.
KEGGisce:YDL066W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57229 Genomic DNA. Translation: AAA34703.1.
Z74114 Genomic DNA. Translation: CAA98631.1.
BK006938 Genomic DNA. Translation: DAA11791.1.
PIRiA38610. DCBYIS.
RefSeqiNP_010217.1. NM_001180125.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2QFVX-ray2.30A/B/C/D16-428[»]
2QFWX-ray2.60A/B/C/D/E/F16-428[»]
2QFXX-ray2.70A/B/C/D/E/F16-428[»]
2QFYX-ray2.10A/B/C/D/E/F16-428[»]
ProteinModelPortaliP21954.
SMRiP21954.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31993. 46 interactors.
DIPiDIP-4494N.
IntActiP21954. 19 interactors.
MINTiMINT-510681.

Proteomic databases

MaxQBiP21954.
PRIDEiP21954.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL066W; YDL066W; YDL066W.
GeneIDi851493.
KEGGisce:YDL066W.

Organism-specific databases

EuPathDBiFungiDB:YDL066W.
SGDiS000002224. IDP1.

Phylogenomic databases

GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
InParanoidiP21954.
KOiK00031.
OMAiPENGEPQ.
OrthoDBiEOG092C2D51.

Enzyme and pathway databases

BioCyciYEAST:YDL066W-MONOMER.
BRENDAi1.1.1.42. 984.
SABIO-RKP21954.

Miscellaneous databases

EvolutionaryTraceiP21954.
PROiP21954.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004790. Isocitrate_DH_NADP.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11822. PTHR11822. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000108. IDH_NADP. 1 hit.
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00127. nadp_idh_euk. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiIDHP_YEAST
AccessioniPrimary (citable) accession number: P21954
Secondary accession number(s): D6VRT1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: November 30, 2016
This is version 157 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, 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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: 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.