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P50216

- IDH_CORGL

UniProt

P50216 - IDH_CORGL

Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 92 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      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.

    Enzyme regulationi

    Weakly inhibited by oxaloacetate, 2-oxoglutarate, and citrate. Severely inhibited by oxaloacetate plus glyoxylate.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei133 – 1331NADPBy similarity
    Binding sitei143 – 1431SubstrateBy similarity
    Sitei253 – 2531Critical for catalysisBy similarity
    Metal bindingi346 – 3461Magnesium or manganese1 Publication
    Sitei416 – 4161Critical for catalysisBy similarity
    Binding sitei543 – 5431SubstrateBy similarity
    Metal bindingi544 – 5441Magnesium or manganese1 Publication
    Metal bindingi548 – 5481Magnesium or manganese1 Publication
    Binding sitei585 – 5851NADPBy similarity
    Binding sitei645 – 6451NADPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi80 – 856NADPBy similarity
    Nucleotide bindingi580 – 5812NADPBy similarity
    Nucleotide bindingi596 – 5983NADPBy similarity

    GO - Molecular functioni

    1. isocitrate dehydrogenase (NADP+) activity Source: UniProtKB-EC
    2. metal ion binding Source: UniProtKB-KW

    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, Metal-binding, NADP

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
    Short name:
    IDH
    Alternative name(s):
    Oxalosuccinate decarboxylase
    Gene namesi
    Name:icd
    Ordered Locus Names:Cgl0664, cg0766
    OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
    Taxonomic identifieri196627 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeCorynebacteriaceaeCorynebacterium
    ProteomesiUP000000582: Chromosome, UP000001009: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 738738Isocitrate dehydrogenase [NADP]PRO_0000083595Add
    BLAST

    Keywords - PTMi

    Phosphoprotein

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    STRINGi196627.cg0766.

    Structurei

    Secondary structure

    1
    738
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 86
    Helixi11 – 2919
    Turni30 – 323
    Beta strandi34 – 396
    Helixi42 – 476
    Helixi51 – 533
    Turni56 – 583
    Helixi63 – 708
    Beta strandi77 – 804
    Helixi88 – 10013
    Helixi115 – 12511
    Beta strandi128 – 1303
    Helixi132 – 1365
    Beta strandi141 – 1444
    Helixi147 – 1559
    Beta strandi170 – 1723
    Beta strandi175 – 1784
    Helixi179 – 1824
    Beta strandi184 – 1874
    Beta strandi192 – 1998
    Beta strandi205 – 21410
    Beta strandi219 – 2257
    Helixi227 – 24418
    Beta strandi247 – 2504
    Turni254 – 2563
    Helixi260 – 27213
    Helixi274 – 28613
    Helixi294 – 3029
    Helixi308 – 32114
    Beta strandi327 – 3293
    Helixi330 – 3323
    Beta strandi342 – 3443
    Helixi345 – 35410
    Turni355 – 3573
    Beta strandi358 – 3603
    Beta strandi366 – 3727
    Helixi376 – 39217
    Turni397 – 3993
    Beta strandi405 – 4073
    Turni410 – 4123
    Helixi414 – 4174
    Helixi419 – 4213
    Beta strandi422 – 4243
    Beta strandi427 – 4348
    Beta strandi440 – 4467
    Beta strandi451 – 4577
    Helixi459 – 47618
    Beta strandi480 – 4834
    Helixi489 – 50214
    Beta strandi512 – 5154
    Helixi517 – 52913
    Beta strandi535 – 5384
    Helixi540 – 55516
    Beta strandi558 – 5603
    Beta strandi562 – 5676
    Beta strandi572 – 5754
    Helixi583 – 59210
    Helixi600 – 61718
    Helixi620 – 63819
    Helixi652 – 66918
    Helixi674 – 70027
    Beta strandi711 – 7133
    Helixi716 – 7238
    Helixi727 – 7359

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2B0TX-ray1.75A1-738[»]
    3MBCX-ray1.90A/B1-738[»]
    ProteinModelPortaliP50216.
    SMRiP50216. Positions 2-736.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP50216.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni130 – 1378Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the monomeric-type IDH family.Curated

    Phylogenomic databases

    eggNOGiCOG2838.
    HOGENOMiHOG000240860.
    KOiK00031.
    OMAiQVQEENH.
    OrthoDBiEOG6DVJPP.

    Family and domain databases

    Gene3Di3.40.718.10. 3 hits.
    InterProiIPR004436. Isocitrate_DH_NADP_mono.
    IPR024084. IsoPropMal-DH-like_dom.
    [Graphical view]
    PfamiPF03971. IDH. 1 hit.
    [Graphical view]
    PIRSFiPIRSF009407. IDH_monmr. 1 hit.
    TIGRFAMsiTIGR00178. monomer_idh. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P50216-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAKIIWTRTD EAPLLATYSL KPVVEAFAAT AGIEVETRDI SLAGRILAQF    50
    PERLTEDQKV GNALAELGEL AKTPEANIIK LPNISASVPQ LKAAIKELQD 100
    QGYDIPELPD NATTDEEKDI LARYNAVKGS AVNPVLREGN SDRRAPIAVK 150
    NFVKKFPHRM GEWSADSKTN VATMDANDFR HNEKSIILDA ADEVQIKHIA 200
    ADGTETILKD SLKLLEGEVL DGTVLSAKAL DAFLLEQVAR AKAEGILFSA 250
    HLKATMMKVS DPIIFGHVVR AYFADVFAQY GEQLLAAGLN GENGLAAILS 300
    GLESLDNGEE IKAAFEKGLE DGPDLAMVNS ARGITNLHVP SDVIVDASMP 350
    AMIRTSGHMW NKDDQEQDTL AIIPDSSYAG VYQTVIEDCR KNGAFDPTTM 400
    GTVPNVGLMA QKAEEYGSHD KTFRIEADGV VQVVSSNGDV LIEHDVEAND 450
    IWRACQVKDA PIQDWVKLAV TRSRLSGMPA VFWLDPERAH DRNLASLVEK 500
    YLADHDTEGL DIQILSPVEA TQLSIDRIRR GEDTISVTGN VLRDYNTDLF 550
    PILELGTSAK MLSVVPLMAG GGLFETGAGG SAPKHVQQVQ EENHLRWDSL 600
    GEFLALAESF RHELNNNGNT KAGVLADALD KATEKLLNEE KSPSRKVGEI 650
    DNRGSHFWLT KFWADELAAQ TEDADLAATF APVAEALNTG AADIDAALLA 700
    VQGGATDLGG YYSPNEEKLT NIMRPVAQFN EIVDALKK 738
    Length:738
    Mass (Da):80,081
    Last modified:October 1, 1996 - v1
    Checksum:iEAC4C5FA38C33F63
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X71489 Genomic DNA. Translation: CAA50590.1.
    BA000036 Genomic DNA. Translation: BAB98057.1.
    BX927149 Genomic DNA. Translation: CAF19369.1.
    PIRiI40719.
    RefSeqiNP_599896.1. NC_003450.3.
    WP_011013800.1. NC_006958.1.
    YP_224955.1. NC_006958.1.

    Genome annotation databases

    EnsemblBacteriaiBAB98057; BAB98057; BAB98057.
    CAF19369; CAF19369; cg0766.
    GeneIDi1018663.
    KEGGicgb:cg0766.
    cgl:NCgl0634.
    PATRICi21493369. VBICorGlu203724_0650.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X71489 Genomic DNA. Translation: CAA50590.1 .
    BA000036 Genomic DNA. Translation: BAB98057.1 .
    BX927149 Genomic DNA. Translation: CAF19369.1 .
    PIRi I40719.
    RefSeqi NP_599896.1. NC_003450.3.
    WP_011013800.1. NC_006958.1.
    YP_224955.1. NC_006958.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2B0T X-ray 1.75 A 1-738 [» ]
    3MBC X-ray 1.90 A/B 1-738 [» ]
    ProteinModelPortali P50216.
    SMRi P50216. Positions 2-736.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 196627.cg0766.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAB98057 ; BAB98057 ; BAB98057 .
    CAF19369 ; CAF19369 ; cg0766 .
    GeneIDi 1018663.
    KEGGi cgb:cg0766.
    cgl:NCgl0634.
    PATRICi 21493369. VBICorGlu203724_0650.

    Phylogenomic databases

    eggNOGi COG2838.
    HOGENOMi HOG000240860.
    KOi K00031.
    OMAi QVQEENH.
    OrthoDBi EOG6DVJPP.

    Miscellaneous databases

    EvolutionaryTracei P50216.

    Family and domain databases

    Gene3Di 3.40.718.10. 3 hits.
    InterProi IPR004436. Isocitrate_DH_NADP_mono.
    IPR024084. IsoPropMal-DH-like_dom.
    [Graphical view ]
    Pfami PF03971. IDH. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF009407. IDH_monmr. 1 hit.
    TIGRFAMsi TIGR00178. monomer_idh. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme."
      Eikmanns B.J., Rittmann D., Sahm H.
      J. Bacteriol. 177:774-782(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    2. "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes."
      Ikeda M., Nakagawa S.
      Appl. Microbiol. Biotechnol. 62:99-109(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    4. "Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase."
      Imabayashi F., Aich S., Prasad L., Delbaere L.T.
      Proteins 63:100-112(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, SUBUNIT.

    Entry informationi

    Entry nameiIDH_CORGL
    AccessioniPrimary (citable) accession number: P50216
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 92 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3