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O29610

- IDH_ARCFU

UniProt

O29610 - IDH_ARCFU

Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 107 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      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

    Kineticsi

    1. KM=118 µM for D,L-isocitrate
    2. KM=30 µM for NADP
    3. KM=5.4 mM for NAD

    Vmax=141 µmol/min/mg enzyme towards NADP at 60 degrees Celsius

    Vmax=14.5 µmol/min/mg enzyme towards NAD

    pH dependencei

    Optimum pH is 8.6.

    Temperature dependencei

    Optimum temperature is 90 degrees Celsius. Thermostable.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei100 – 1001NADPBy similarity
    Binding sitei109 – 1091SubstrateBy similarity
    Binding sitei111 – 1111SubstrateBy similarity
    Binding sitei115 – 1151SubstrateBy similarity
    Binding sitei125 – 1251SubstrateBy similarity
    Binding sitei149 – 1491SubstrateBy similarity
    Sitei156 – 1561Critical for catalysisBy similarity
    Sitei223 – 2231Critical for catalysisBy similarity
    Metal bindingi301 – 3011Magnesium or manganeseBy similarity
    Binding sitei346 – 3461NADP; via amide nitrogen and carbonyl oxygenBy similarity
    Binding sitei385 – 3851NADPBy similarity
    Binding sitei389 – 3891NADPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi333 – 3397NADPBy 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

    Enzyme and pathway databases

    BioCyciAFUL224325:GJBC-662-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
    Ordered Locus Names:AF_0647
    OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
    Taxonomic identifieri224325 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
    ProteomesiUP000002199: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 412412Isocitrate dehydrogenase [NADP]PRO_0000083572Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei109 – 1091PhosphoserineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Interactioni

    Subunit structurei

    Homodimer.

    Protein-protein interaction databases

    STRINGi224325.AF0647.

    Structurei

    Secondary structure

    1
    412
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi16 – 183
    Beta strandi21 – 233
    Beta strandi26 – 338
    Helixi39 – 5719
    Beta strandi62 – 654
    Helixi70 – 767
    Helixi82 – 9110
    Beta strandi93 – 964
    Beta strandi103 – 1086
    Helixi109 – 1179
    Beta strandi122 – 1287
    Beta strandi136 – 1383
    Helixi140 – 1423
    Beta strandi144 – 1507
    Beta strandi152 – 1543
    Helixi155 – 1573
    Helixi166 – 17914
    Beta strandi187 – 1959
    Helixi196 – 21217
    Beta strandi216 – 2227
    Turni224 – 2263
    Turni228 – 2303
    Helixi231 – 24515
    Turni247 – 2493
    Helixi253 – 2608
    Beta strandi269 – 2757
    Helixi276 – 2783
    Helixi279 – 2857
    Helixi287 – 2893
    Beta strandi292 – 2954
    Helixi297 – 31014
    Helixi314 – 3163
    Beta strandi318 – 3236
    Beta strandi326 – 3338
    Turni338 – 3414
    Helixi348 – 36013
    Helixi364 – 37916
    Helixi385 – 3917
    Beta strandi393 – 3953
    Helixi398 – 41114

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2IV0X-ray2.50A/B1-412[»]
    ProteinModelPortaliO29610.
    SMRiO29610. Positions 1-412.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO29610.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0538.
    KOiK00031.
    OMAiCLRPIRY.

    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.

    O29610-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQYEKVKPPE NGEKIRYENG KLIVPDNPII PYFEGDGIGK DVVPAAIRVL    50
    DAAADKIGKE VVWFQVYAGE DAYKLYGNYL PDDTLNAIKE FRVALKGPLT 100
    TPVGGGYRSL NVTIRQVLDL YANVRPVYYL KGVPSPIKHP EKVNFVIFRE 150
    NTEDVYAGIE WPRGSEEALK LIRFLKNEFG VTIREDSGIG IKPISEFATK 200
    RLVRMAIRYA IENNRKSVTL VHKGNIMKYT EGAFRDWGYE VAKQEFGEYC 250
    ITEDELWDKY GGKQPEGKIV VKDRIADNMF QQILTRTDEY DVIALPNLNG 300
    DYLSDAAAAL IGGLGIAPGS NIGDGIGVFE PVHGSAPKYA GQNKVNPTAE 350
    ILTGALMFEY IGWKDASEMI KKAVEMTISS GIVTYDIHRH MGGTKVGTRE 400
    FAEAVVENLQ SL 412
    Length:412
    Mass (Da):45,842
    Last modified:January 1, 1998 - v1
    Checksum:iA2E1A3AA7662D3EA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z96105 Genomic DNA. Translation: CAB09535.1.
    AE000782 Genomic DNA. Translation: AAB90591.1.
    PIRiG69330.
    RefSeqiNP_069481.1. NC_000917.1.
    WP_010878150.1. NC_000917.1.

    Genome annotation databases

    EnsemblBacteriaiAAB90591; AAB90591; AF_0647.
    GeneIDi1483865.
    KEGGiafu:AF0647.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z96105 Genomic DNA. Translation: CAB09535.1 .
    AE000782 Genomic DNA. Translation: AAB90591.1 .
    PIRi G69330.
    RefSeqi NP_069481.1. NC_000917.1.
    WP_010878150.1. NC_000917.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2IV0 X-ray 2.50 A/B 1-412 [» ]
    ProteinModelPortali O29610.
    SMRi O29610. Positions 1-412.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224325.AF0647.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAB90591 ; AAB90591 ; AF_0647 .
    GeneIDi 1483865.
    KEGGi afu:AF0647.

    Phylogenomic databases

    eggNOGi COG0538.
    KOi K00031.
    OMAi CLRPIRY.

    Enzyme and pathway databases

    BioCyci AFUL224325:GJBC-662-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O29610.

    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. "Biochemical and phylogenetic characterization of isocitrate dehydrogenase from a hyperthermophilic archaeon, Archaeoglobus fulgidus."
      Steen I.H., Lien T., Birkeland N.-K.
      Arch. Microbiol. 168:412-420(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-27, CHARACTERIZATION.
      Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
    2. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
      Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
      , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
      Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.

    Entry informationi

    Entry nameiIDH_ARCFU
    AccessioniPrimary (citable) accession number: O29610
    Secondary accession number(s): O31221
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 29, 2001
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 107 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, 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

    External Data

    Dasty 3