Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P39126

- IDH_BACSU

UniProt

P39126 - IDH_BACSU

Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    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 sitei95 – 951NADPBy similarity
    Binding sitei96 – 961Substrate
    Binding sitei104 – 1041Substrate
    Binding sitei106 – 1061Substrate
    Binding sitei110 – 1101Substrate
    Binding sitei120 – 1201SubstrateBy similarity
    Binding sitei144 – 1441Substrate
    Sitei151 – 1511Critical for catalysisBy similarity
    Sitei221 – 2211Critical for catalysisBy similarity
    Metal bindingi311 – 3111Magnesium or manganeseBy similarity
    Binding sitei358 – 3581NADP; via amide nitrogen and carbonyl oxygenBy similarity
    Binding sitei397 – 3971NADPBy similarity
    Binding sitei401 – 4011NADPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi345 – 3517NADPBy similarity

    GO - Molecular functioni

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

    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

    Enzyme and pathway databases

    BioCyciBSUB:BSU29130-MONOMER.

    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
    Synonyms:citC
    Ordered Locus Names:BSU29130
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU29130. [Micado]

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 423423Isocitrate dehydrogenase [NADP]PRO_0000083549Add
    BLAST

    Proteomic databases

    PaxDbiP39126.
    PRIDEiP39126.

    PTM databases

    PhosSiteiP0204106.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    mdhP498143EBI-7829570,EBI-7827708

    Protein-protein interaction databases

    IntActiP39126. 2 interactions.
    MINTiMINT-1711252.
    STRINGi224308.BSU29130.

    Structurei

    Secondary structure

    1
    423
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 53
    Beta strandi8 – 103
    Beta strandi13 – 153
    Beta strandi18 – 258
    Helixi31 – 5020
    Beta strandi57 – 604
    Helixi65 – 717
    Helixi77 – 8610
    Beta strandi88 – 914
    Beta strandi98 – 1025
    Helixi105 – 1128
    Beta strandi117 – 1237
    Beta strandi131 – 1333
    Helixi135 – 1373
    Beta strandi139 – 1457
    Helixi149 – 1524
    Helixi161 – 17313
    Helixi182 – 1843
    Beta strandi185 – 1939
    Helixi194 – 21118
    Beta strandi214 – 2207
    Turni222 – 2243
    Turni226 – 2283
    Helixi229 – 24416
    Helixi245 – 2473
    Beta strandi248 – 2503
    Helixi251 – 27525
    Beta strandi279 – 2857
    Helixi286 – 29510
    Helixi297 – 2993
    Beta strandi301 – 3055
    Helixi307 – 32014
    Turni324 – 3263
    Beta strandi328 – 3325
    Turni334 – 3363
    Beta strandi339 – 3446
    Helixi349 – 3513
    Turni352 – 3554
    Helixi360 – 37314
    Helixi376 – 39116
    Helixi397 – 4004
    Beta strandi403 – 4053
    Helixi411 – 42010

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HQSX-ray1.55A/B1-423[»]
    ProteinModelPortaliP39126.
    SMRiP39126. Positions 1-423.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39126.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0538.
    HOGENOMiHOG000021113.
    KOiK00031.
    OMAiCLRPIRY.
    OrthoDBiEOG6SNDTP.
    PhylomeDBiP39126.

    Family and domain databases

    Gene3Di3.40.718.10. 1 hit.
    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.

    P39126-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAQGEKITVS NGVLNVPNNP IIPFIEGDGT GPDIWNAASK VLEAAVEKAY    50
    KGEKKITWKE VYAGEKAYNK TGEWLPAETL DVIREYFIAI KGPLTTPVGG 100
    GIRSLNVALR QELDLFVCLR PVRYFTGVPS PVKRPEDTDM VIFRENTEDI 150
    YAGIEYAKGS EEVQKLISFL QNELNVNKIR FPETSGIGIK PVSEEGTSRL 200
    VRAAIDYAIE HGRKSVTLVH KGNIMKFTEG AFKNWGYELA EKEYGDKVFT 250
    WAQYDRIAEE QGKDAANKAQ SEAEAAGKII IKDSIADIFL QQILTRPNEF 300
    DVVATMNLNG DYISDALAAQ VGGIGIAPGA NINYETGHAI FEATHGTAPK 350
    YAGLDKVNPS SVILSGVLLL EHLGWNEAAD LVIKSMEKTI ASKVVTYDFA 400
    RLMDGATEVK CSEFGEELIK NMD 423
    Length:423
    Mass (Da):46,418
    Last modified:February 1, 1995 - v1
    Checksum:iCC69E694EB66D0D8
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U05257 Genomic DNA. Translation: AAA96342.1.
    AF008220 Genomic DNA. Translation: AAC00346.1.
    AL009126 Genomic DNA. Translation: CAB14873.1.
    PIRiI40382.
    RefSeqiNP_390791.1. NC_000964.3.

    Genome annotation databases

    EnsemblBacteriaiCAB14873; CAB14873; BSU29130.
    GeneIDi938183.
    KEGGibsu:BSU29130.
    PATRICi18977720. VBIBacSub10457_3048.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U05257 Genomic DNA. Translation: AAA96342.1 .
    AF008220 Genomic DNA. Translation: AAC00346.1 .
    AL009126 Genomic DNA. Translation: CAB14873.1 .
    PIRi I40382.
    RefSeqi NP_390791.1. NC_000964.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1HQS X-ray 1.55 A/B 1-423 [» ]
    ProteinModelPortali P39126.
    SMRi P39126. Positions 1-423.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P39126. 2 interactions.
    MINTi MINT-1711252.
    STRINGi 224308.BSU29130.

    PTM databases

    PhosSitei P0204106.

    Proteomic databases

    PaxDbi P39126.
    PRIDEi P39126.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB14873 ; CAB14873 ; BSU29130 .
    GeneIDi 938183.
    KEGGi bsu:BSU29130.
    PATRICi 18977720. VBIBacSub10457_3048.

    Organism-specific databases

    GenoListi BSU29130. [Micado ]

    Phylogenomic databases

    eggNOGi COG0538.
    HOGENOMi HOG000021113.
    KOi K00031.
    OMAi CLRPIRY.
    OrthoDBi EOG6SNDTP.
    PhylomeDBi P39126.

    Enzyme and pathway databases

    BioCyci BSUB:BSU29130-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P39126.

    Family and domain databases

    Gene3Di 3.40.718.10. 1 hit.
    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. "Identification of two distinct Bacillus subtilis citrate synthase genes."
      Jin S., Sonenshein A.L.
      J. Bacteriol. 176:4669-4679(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168 / SMY.
    2. "Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region."
      Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.
      Microbiology 143:3431-3441(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    4. "Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/phosphatase."
      Singh S.K., Miller S.P., Dean A., Banaszak L.J., LaPorte D.C.
      J. Biol. Chem. 277:7567-7573(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION.
    5. "Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase."
      Singh S.K., Matsuno K., LaPorte D.C., Banaszak L.J.
      J. Biol. Chem. 276:26154-26163(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH CITRATE, SUBUNIT.

    Entry informationi

    Entry nameiIDH_BACSU
    AccessioniPrimary (citable) accession number: P39126
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 122 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The enzyme can be phosphorylated in vitro by the E.coli isocitrate dehydrogenase kinase/phosphatase, but B.subtilis lacks such an enzyme.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3