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P21954

- IDHP_YEAST

UniProt

P21954 - IDHP_YEAST

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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: 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 Mg(2+) or Mn(2+) ion per subunit.By similarity

Enzyme regulationi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei93 – 931SubstrateBy similarity
Binding sitei98 – 981NADPBy similarity
Binding sitei125 – 1251SubstrateBy similarity
Binding sitei148 – 1481SubstrateBy similarity
Sitei155 – 1551Critical for catalysisBy similarity
Sitei229 – 2291Critical for catalysisBy similarity
Metal bindingi269 – 2691Magnesium or manganeseBy similarity
Binding sitei277 – 2771NADPBy similarity
Metal bindingi292 – 2921Magnesium or manganeseBy similarity
Binding sitei345 – 3451NADP; via amide nitrogen and carbonyl oxygenBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi91 – 933NADPBy similarity
Nucleotide bindingi327 – 3326NADPBy similarity

GO - Molecular functioni

  1. isocitrate dehydrogenase (NADP+) activity Source: SGD
  2. magnesium ion binding Source: InterPro
  3. NAD binding Source: InterPro

GO - Biological processi

  1. glutamate biosynthetic process Source: SGD
  2. glyoxylate cycle Source: UniProtKB-KW
  3. isocitrate metabolic process Source: InterPro
  4. 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.
ReactomeiREACT_207320. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
REACT_227890. NADPH regeneration.
REACT_245486. Citric acid cycle (TCA cycle).
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
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

CYGDiYDL066w.
SGDiS000002224. IDP1.

Subcellular locationi

GO - Cellular componenti

  1. mitochondrial nucleoid Source: SGD
  2. mitochondrion Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 1616Mitochondrion1 PublicationAdd
BLAST
Chaini17 – 428412Isocitrate dehydrogenase [NADP], mitochondrialPRO_0000014426Add
BLAST

Proteomic databases

MaxQBiP21954.
PaxDbiP21954.
PeptideAtlasiP21954.
PRIDEiP21954.

Expressioni

Inductioni

By growth with glucose as a carbon source.

Gene expression databases

GenevestigatoriP21954.

Interactioni

Subunit structurei

Homodimer.

Binary interactionsi

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

Protein-protein interaction databases

BioGridi31993. 42 interactions.
DIPiDIP-4494N.
IntActiP21954. 18 interactions.
MINTiMINT-510681.
STRINGi4932.YDL066W.

Structurei

Secondary structure

1
428
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi26 – 305Combined sources
Helixi33 – 4614Combined sources
Turni47 – 504Combined sources
Beta strandi55 – 595Combined sources
Helixi62 – 676Combined sources
Turni68 – 703Combined sources
Helixi71 – 8313Combined sources
Beta strandi84 – 885Combined sources
Helixi96 – 1016Combined sources
Helixi111 – 1199Combined sources
Beta strandi121 – 1277Combined sources
Beta strandi142 – 1498Combined sources
Helixi153 – 1564Combined sources
Beta strandi158 – 1625Combined sources
Beta strandi164 – 17512Combined sources
Turni177 – 1793Combined sources
Beta strandi183 – 19210Combined sources
Beta strandi194 – 2029Combined sources
Helixi203 – 22018Combined sources
Beta strandi224 – 2285Combined sources
Turni230 – 2323Combined sources
Helixi236 – 25116Combined sources
Helixi253 – 2597Combined sources
Beta strandi263 – 2675Combined sources
Helixi268 – 27710Combined sources
Beta strandi280 – 2867Combined sources
Helixi288 – 30215Combined sources
Beta strandi307 – 3137Combined sources
Beta strandi315 – 3184Combined sources
Beta strandi320 – 3234Combined sources
Helixi330 – 3378Combined sources
Helixi347 – 36418Combined sources
Helixi367 – 38519Combined sources
Helixi392 – 3976Combined sources
Helixi403 – 4053Combined sources
Helixi409 – 42618Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 17-427.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21954.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni110 – 1167Substrate bindingBy similarity

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
InParanoidiP21954.
KOiK00031.
OMAiTRIIWDK.
OrthoDBiEOG7G4QQD.

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.
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 .
PIRi A38610. DCBYIS.
RefSeqi NP_010217.1. NM_001180125.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2QFV X-ray 2.30 A/B/C/D 16-428 [» ]
2QFW X-ray 2.60 A/B/C/D/E/F 16-428 [» ]
2QFX X-ray 2.70 A/B/C/D/E/F 16-428 [» ]
2QFY X-ray 2.10 A/B/C/D/E/F 16-428 [» ]
ProteinModelPortali P21954.
SMRi P21954. Positions 17-427.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31993. 42 interactions.
DIPi DIP-4494N.
IntActi P21954. 18 interactions.
MINTi MINT-510681.
STRINGi 4932.YDL066W.

Proteomic databases

MaxQBi P21954.
PaxDbi P21954.
PeptideAtlasi P21954.
PRIDEi P21954.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDL066W ; YDL066W ; YDL066W .
GeneIDi 851493.
KEGGi sce:YDL066W.

Organism-specific databases

CYGDi YDL066w.
SGDi S000002224. IDP1.

Phylogenomic databases

eggNOGi COG0538.
GeneTreei ENSGT00390000012547.
HOGENOMi HOG000019858.
InParanoidi P21954.
KOi K00031.
OMAi TRIIWDK.
OrthoDBi EOG7G4QQD.

Enzyme and pathway databases

BioCyci YEAST:YDL066W-MONOMER.
Reactomei REACT_207320. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
REACT_227890. NADPH regeneration.
REACT_245486. Citric acid cycle (TCA cycle).
SABIO-RK P21954.

Miscellaneous databases

EvolutionaryTracei P21954.
NextBioi 968825.
PROi P21954.

Gene expression databases

Genevestigatori P21954.

Family and domain databases

Gene3Di 3.40.718.10. 1 hit.
InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004790. Isocitrate_DH_NADP.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view ]
PANTHERi PTHR11822. PTHR11822. 1 hit.
Pfami PF00180. Iso_dh. 1 hit.
[Graphical view ]
PIRSFi PIRSF000108. IDH_NADP. 1 hit.
TIGRFAMsi TIGR00127. nadp_idh_euk. 1 hit.
PROSITEi PS00470. IDH_IMDH. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation, nucleotide sequence, and disruption of the Saccharomyces cerevisiae gene encoding mitochondrial NADP(H)-specific isocitrate dehydrogenase."
    Haselbeck R.J., McAlister-Henn L.
    J. Biol. Chem. 266:2339-2345(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 17-36.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(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.

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 26, 2014
This is version 139 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

External Data

Dasty 3