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P21954

- IDHP_YEAST

UniProt

P21954 - IDHP_YEAST

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Protein
Isocitrate dehydrogenase [NADP], mitochondrial
Gene
IDP1, YDL066W
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

Binds 1 magnesium or manganese 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 – 931Substrate By similarity
Binding sitei98 – 981NADP By similarity
Binding sitei125 – 1251Substrate By similarity
Binding sitei148 – 1481Substrate By similarity
Sitei155 – 1551Critical for catalysis By similarity
Sitei229 – 2291Critical for catalysis By similarity
Metal bindingi269 – 2691Magnesium or manganese By similarity
Binding sitei277 – 2771NADP By similarity
Metal bindingi292 – 2921Magnesium or manganese By similarity
Binding sitei345 – 3451NADP; via amide nitrogen and carbonyl oxygen By similarity

Regions

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

GO - Molecular functioni

  1. NAD binding Source: InterPro
  2. isocitrate dehydrogenase (NADP+) activity Source: SGD
  3. magnesium ion binding Source: InterPro
  4. protein binding Source: IntAct
Complete GO annotation...

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.
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 Publication
Add
BLAST
Chaini17 – 428412Isocitrate dehydrogenase [NADP], mitochondrial
PRO_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. 40 interactions.
DIPiDIP-4494N.
IntActiP21954. 18 interactions.
MINTiMINT-510681.
STRINGi4932.YDL066W.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiP21954.

Family & Domainsi

Region

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

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
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

MSMLSRRLFS TSRLAAFSKI KVKQPVVELD GDEMTRIIWD KIKKKLILPY    50
LDVDLKYYDL SVESRDATSD KITQDAAEAI KKYGVGIKCA TITPDEARVK 100
EFNLHKMWKS PNGTIRNILG GTVFREPIVI PRIPRLVPRW EKPIIIGRHA 150
HGDQYKATDT LIPGPGSLEL VYKPSDPTTA QPQTLKVYDY KGSGVAMAMY 200
NTDESIEGFA HSSFKLAIDK KLNLFLSTKN TILKKYDGRF KDIFQEVYEA 250
QYKSKFEQLG IHYEHRLIDD MVAQMIKSKG GFIMALKNYD GDVQSDIVAQ 300
GFGSLGLMTS ILVTPDGKTF ESEAAHGTVT RHYRKYQKGE ETSTNSIASI 350
FAWSRGLLKR GELDNTPALC KFANILESAT LNTVQQDGIM TKDLALACGN 400
NERSAYVTTE EFLDAVEKRL QKEIKSIE 428
Length:428
Mass (Da):48,190
Last modified:August 1, 1991 - v1
Checksum:i7F885785B8682416
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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:
PDBe
RCSB PDB
PDBj
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...

Protein-protein interaction databases

BioGridi 31993. 40 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.
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.
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: September 3, 2014
This is version 136 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

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