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P80046

- IDH_SYNY3

UniProt

P80046 - IDH_SYNY3

Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 103 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Catalytic activityi

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

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.By similarity

    Enzyme regulationi

    Inhibition of this enzyme by phosphorylation regulates the branch point between the Krebs cycle and the glyoxylate bypass, which is an alternate route that accumulates carbon for biosynthesis when acetate is the sole carbon source for growth.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei104 – 1041NADPBy similarity
    Binding sitei113 – 1131SubstrateBy similarity
    Binding sitei115 – 1151SubstrateBy similarity
    Binding sitei119 – 1191SubstrateBy similarity
    Binding sitei129 – 1291SubstrateBy similarity
    Binding sitei153 – 1531SubstrateBy similarity
    Sitei160 – 1601Critical for catalysisBy similarity
    Sitei237 – 2371Critical for catalysisBy similarity
    Metal bindingi362 – 3621Magnesium or manganeseBy similarity
    Binding sitei407 – 4071NADP; via amide nitrogen and carbonyl oxygenBy similarity
    Binding sitei446 – 4461NADPBy similarity
    Binding sitei450 – 4501NADPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi394 – 4007NADPBy 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. glyoxylate cycle Source: UniProtKB-KW
    2. tricarboxylic acid cycle Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glyoxylate bypass, Tricarboxylic acid cycle

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, NADP

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
    Short name:
    IDH
    Alternative name(s):
    IDP
    NADP(+)-specific ICDH
    Oxalosuccinate decarboxylase
    Gene namesi
    Name:icd
    Ordered Locus Names:slr1289
    OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
    Taxonomic identifieri1111708 [NCBI]
    Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
    ProteomesiUP000001425: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 475475Isocitrate dehydrogenase [NADP]PRO_0000083570Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei113 – 1131PhosphoserineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiP80046.
    PRIDEiP80046.

    Interactioni

    Subunit structurei

    Homodimer.

    Protein-protein interaction databases

    IntActiP80046. 2 interactions.
    STRINGi1148.slr1289.

    Structurei

    3D structure databases

    ProteinModelPortaliP80046.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0538.
    HOGENOMiHOG000021113.
    KOiK00031.
    OrthoDBiEOG6SNDTP.
    PhylomeDBiP80046.

    Family and domain databases

    Gene3Di3.40.718.10. 2 hits.
    InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
    IPR001804. Isocitrate/isopropylmalate_DH.
    IPR004439. Isocitrate_DH_NADP_dimer_prok.
    IPR024084. IsoPropMal-DH-like_dom.
    [Graphical view]
    PANTHERiPTHR11835. PTHR11835. 1 hit.
    PfamiPF00180. Iso_dh. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00183. prok_nadp_idh. 1 hit.
    PROSITEiPS00470. IDH_IMDH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P80046-1 [UniParc]FASTAAdd to Basket

    « Hide

    MYEKLQPPSV GSKITFVAGK PVVPNDPIIP YIRGDGTGVD IWPATELVIN    50
    AAIAKAYGGR EEINWFKVYA GDEACELYGT YQIFPEDTLT AIKEYGVAIK 100
    GPLTTPVGGG IRSLNVALRQ IFDLYTCVRP CRYYPGTPSP HKTPEKLDII 150
    VYRENTEDIY LGIEWAEGTE GAKKLIAYLN DELIPTTPAL GKKQIRLDSG 200
    IGIKPISKTG SQRLVRRAIL HAKRLPKAKQ MVTLVHKGNI MKFTEGPFRD 250
    WGYELATTEF RAECVTERES WICGNKESNP DLTIEANAHM IDPGYDTLTE 300
    EKQAVIKQEV EQVLNSIWES HGNGQWKEKV MVNDRIADSI FQQIQTRPDE 350
    YSILATMNLN GDYLSDAAAA VVGGLGMGPG ANIGDSAAIF EATHGTAPKH 400
    AGLDRINPGS VILSGVMMLE FMGWQEAADL IKKGIGAAIA NREVTYDLAR 450
    LMEPKVDKPL KCSEFAQAIV SHFDD 475
    Length:475
    Mass (Da):52,275
    Last modified:November 1, 1997 - v2
    Checksum:i6F3254A8BBA75F92
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti60 – 623REE → ERK in BAA16835. (PubMed:8905231)Curated
    Sequence conflicti83 – 842IF → YL in BAA16835. (PubMed:8905231)Curated
    Sequence conflicti223 – 2231K → L in BAA16835. (PubMed:8905231)Curated
    Sequence conflicti247 – 2471P → A in BAA16835. (PubMed:8905231)Curated
    Sequence conflicti273 – 2731C → L in BAA16835. (PubMed:8905231)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X83563 Genomic DNA. Translation: CAA58549.1.
    BA000022 Genomic DNA. Translation: BAA16835.1.
    PIRiS74684.
    RefSeqiNP_440155.1. NC_000911.1.
    YP_005650212.1. NC_017277.1.
    YP_007450038.1. NC_020286.1.

    Genome annotation databases

    EnsemblBacteriaiBAA16835; BAA16835; BAA16835.
    GeneIDi953454.
    KEGGisyn:slr1289.
    syy:SYNGTS_0259.
    syz:MYO_12610.
    PATRICi23837428. VBISynSp132158_0286.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X83563 Genomic DNA. Translation: CAA58549.1 .
    BA000022 Genomic DNA. Translation: BAA16835.1 .
    PIRi S74684.
    RefSeqi NP_440155.1. NC_000911.1.
    YP_005650212.1. NC_017277.1.
    YP_007450038.1. NC_020286.1.

    3D structure databases

    ProteinModelPortali P80046.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P80046. 2 interactions.
    STRINGi 1148.slr1289.

    Proteomic databases

    PaxDbi P80046.
    PRIDEi P80046.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA16835 ; BAA16835 ; BAA16835 .
    GeneIDi 953454.
    KEGGi syn:slr1289.
    syy:SYNGTS_0259.
    syz:MYO_12610.
    PATRICi 23837428. VBISynSp132158_0286.

    Phylogenomic databases

    eggNOGi COG0538.
    HOGENOMi HOG000021113.
    KOi K00031.
    OrthoDBi EOG6SNDTP.
    PhylomeDBi P80046.

    Family and domain databases

    Gene3Di 3.40.718.10. 2 hits.
    InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
    IPR001804. Isocitrate/isopropylmalate_DH.
    IPR004439. Isocitrate_DH_NADP_dimer_prok.
    IPR024084. IsoPropMal-DH-like_dom.
    [Graphical view ]
    PANTHERi PTHR11835. PTHR11835. 1 hit.
    Pfami PF00180. Iso_dh. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00183. prok_nadp_idh. 1 hit.
    PROSITEi PS00470. IDH_IMDH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The NADP+-isocitrate dehydrogenase gene (icd) is nitrogen regulated in cyanobacteria."
      Muro-Pastor M.I., Reyes J.C., Florencio F.J.
      J. Bacteriol. 178:4070-4076(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
      Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
      , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
      DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: PCC 6803 / Kazusa.
    3. "Purification and properties of NADP-isocitrate dehydrogenase from the unicellular cyanobacterium Synechocystis sp. PCC 6803."
      Muro-Pastor M.I., Florencio F.J.
      Eur. J. Biochem. 203:99-105(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-20.

    Entry informationi

    Entry nameiIDH_SYNY3
    AccessioniPrimary (citable) accession number: P80046
    Secondary accession number(s): P72820
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 1, 1992
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 103 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Synechocystis PCC 6803
      Synechocystis (strain PCC 6803): entries and gene names

    External Data

    Dasty 3