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Q9SLK0

- ICDHX_ARATH

UniProt

Q9SLK0 - ICDHX_ARATH

Protein

Peroxisomal isocitrate dehydrogenase [NADP]

Gene

ICDH

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 105 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    May be involved in response to oxidative stresses.By similarity

    Catalytic activityi

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

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei79 – 791SubstrateBy similarity
    Binding sitei84 – 841NADPBy similarity
    Binding sitei111 – 1111SubstrateBy similarity
    Binding sitei134 – 1341SubstrateBy similarity
    Sitei141 – 1411Critical for catalysisBy similarity
    Sitei213 – 2131Critical for catalysisBy similarity
    Metal bindingi253 – 2531Magnesium or manganeseBy similarity
    Binding sitei261 – 2611NADPBy similarity
    Metal bindingi276 – 2761Magnesium or manganeseBy similarity
    Binding sitei329 – 3291NADP; via amide nitrogen and carbonyl oxygenBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi77 – 793NADPBy similarity
    Nucleotide bindingi311 – 3166NADPBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. isocitrate metabolic process Source: InterPro
    2. response to stress Source: UniProtKB-KW
    3. tricarboxylic acid cycle Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Stress response, Tricarboxylic acid cycle

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, NADP

    Enzyme and pathway databases

    BioCyciARA:AT1G54340-MONOMER.
    ReactomeiREACT_214122. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
    REACT_218202. NADPH regeneration.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peroxisomal isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
    Gene namesi
    Name:ICDH
    Ordered Locus Names:At1g54340
    ORF Names:F20D21.16
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 1

    Organism-specific databases

    TAIRiAT1G54340.

    Subcellular locationi

    Peroxisome 2 Publications

    GO - Cellular componenti

    1. peroxisome Source: TAIR
    2. plasma membrane Source: TAIR

    Keywords - Cellular componenti

    Peroxisome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 416416Peroxisomal isocitrate dehydrogenase [NADP]PRO_0000421962Add
    BLAST

    Proteomic databases

    PRIDEiQ9SLK0.

    Expressioni

    Gene expression databases

    ArrayExpressiQ9SLK0.
    GenevestigatoriQ9SLK0.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9SLK0.
    SMRiQ9SLK0. Positions 4-409.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni96 – 1027Substrate bindingBy similarity

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi414 – 4163Peroxisomal targeting signalCurated

    Sequence similaritiesi

    Phylogenomic databases

    HOGENOMiHOG000019858.
    InParanoidiQ9SLK0.
    KOiK00031.
    OMAiEANWRSK.
    PhylomeDBiQ9SLK0.

    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.

    Q9SLK0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEFEKIKVIN PVVEMDGDEM TRVIWKFIKD KLIFPFLELD IKYFDLGLPN    50
    RDFTDDKVTI ETAEATLKYN VAIKCATITP DEARVREFGL KKMWRSPNGT 100
    IRNILNGTVF REPIICRNIP RLVPGWTKPI CIGRHAFGDQ YRATDLIVNE 150
    PGKLKLVFEP SGSSQKTEFE VFNFTGGGVA LAMYNTDESI RAFAESSMYT 200
    AYQKKWPLYL STKNTILKIY DGRFKDIFQE VYEANWRSKY EAAGIWYEHR 250
    LIDDMVAYAM KSEGGYVWAC KNYDGDVQSD FLAQGYGSLG MMTSVLVCPD 300
    GKTIEAEAAH GTVTRHYRVH QKGGETSTNS IASIFAWSRG LAHRAKLDSN 350
    AALLSYTEKL EAACMGTVES GKMTKDLALL IHGAKVRRDQ YVNTEEFIDA 400
    VAWELKRRLL GNNSRL 416
    Length:416
    Mass (Da):47,234
    Last modified:May 1, 2000 - v1
    Checksum:iEEAAAC9E5C6B2FA5
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF316501 mRNA. Translation: AAK06592.1.
    AC005287 Genomic DNA. Translation: AAD25614.1.
    CP002684 Genomic DNA. Translation: AEE33082.1.
    BT025983 mRNA. Translation: ABG25072.1.
    PIRiA96585.
    RefSeqiNP_175836.1. NM_104312.2.
    UniGeneiAt.11811.
    At.37230.

    Genome annotation databases

    EnsemblPlantsiAT1G54340.1; AT1G54340.1; AT1G54340.
    GeneIDi841875.
    KEGGiath:AT1G54340.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF316501 mRNA. Translation: AAK06592.1 .
    AC005287 Genomic DNA. Translation: AAD25614.1 .
    CP002684 Genomic DNA. Translation: AEE33082.1 .
    BT025983 mRNA. Translation: ABG25072.1 .
    PIRi A96585.
    RefSeqi NP_175836.1. NM_104312.2.
    UniGenei At.11811.
    At.37230.

    3D structure databases

    ProteinModelPortali Q9SLK0.
    SMRi Q9SLK0. Positions 4-409.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q9SLK0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G54340.1 ; AT1G54340.1 ; AT1G54340 .
    GeneIDi 841875.
    KEGGi ath:AT1G54340.

    Organism-specific databases

    TAIRi AT1G54340.

    Phylogenomic databases

    HOGENOMi HOG000019858.
    InParanoidi Q9SLK0.
    KOi K00031.
    OMAi EANWRSK.
    PhylomeDBi Q9SLK0.

    Enzyme and pathway databases

    BioCyci ARA:AT1G54340-MONOMER.
    Reactomei REACT_214122. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
    REACT_218202. NADPH regeneration.

    Gene expression databases

    ArrayExpressi Q9SLK0.
    Genevestigatori Q9SLK0.

    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

    1. "Isolation of cDNA encoding NADP-specific isocitrate dehydrogenase from Arabidopsis thaliana."
      Kihara T., Ito N., Koyama H., Hara T.
      Submitted (OCT-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: cv. Columbia.
    2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Arabidopsis ORF clones."
      Shinn P., Chen H., Kim C.J., Quinitio C., Ecker J.R.
      Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms."
      Reumann S., Babujee L., Ma C., Wienkoop S., Siemsen T., Antonicelli G.E., Rasche N., Lueder F., Weckwerth W., Jahn O.
      Plant Cell 19:3170-3193(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 32-51, SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    6. "In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes."
      Reumann S., Quan S., Aung K., Yang P., Manandhar-Shrestha K., Holbrook D., Linka N., Switzenberg R., Wilkerson C.G., Weber A.P., Olsen L.J., Hu J.
      Plant Physiol. 150:125-143(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiICDHX_ARATH
    AccessioniPrimary (citable) accession number: Q9SLK0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 3, 2013
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 105 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3