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P16100

- IDH_AZOVI

UniProt

P16100 - IDH_AZOVI

Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Azotobacter vinelandii
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 97 (01 Oct 2014)
      Sequence version 5 (23 Jan 2007)
      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

    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. The phosphorylation state of this enzyme is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK).

    Temperature dependencei

    Optimum temperature is above 40 degrees Celsius.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei135 – 1351NADP
    Binding sitei145 – 1451Substrate
    Sitei255 – 2551Critical for catalysisBy similarity
    Metal bindingi350 – 3501Magnesium or manganese
    Sitei420 – 4201Critical for catalysisBy similarity
    Binding sitei547 – 5471Substrate
    Metal bindingi548 – 5481Magnesium or manganese
    Metal bindingi552 – 5521Magnesium or manganeseBy similarity
    Binding sitei589 – 5891NADP
    Binding sitei649 – 6491NADP

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi82 – 876NADP
    Nucleotide bindingi584 – 5852NADP
    Nucleotide bindingi600 – 6023NADP

    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, Manganese, Metal-binding, NADP

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13167.

    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
    OrganismiAzotobacter vinelandii
    Taxonomic identifieri354 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeAzotobacter

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 741740Isocitrate dehydrogenase [NADP]PRO_0000083593Add
    BLAST

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PRIDEiP16100.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Structurei

    Secondary structure

    1
    741
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106
    Helixi13 – 3119
    Turni32 – 343
    Beta strandi36 – 416
    Helixi44 – 518
    Helixi53 – 553
    Turni58 – 603
    Helixi65 – 728
    Beta strandi79 – 824
    Helixi90 – 10213
    Helixi117 – 12913
    Beta strandi130 – 1323
    Helixi135 – 1384
    Beta strandi143 – 1464
    Helixi149 – 1579
    Beta strandi172 – 1743
    Beta strandi177 – 1804
    Helixi181 – 1844
    Beta strandi186 – 1894
    Beta strandi192 – 20211
    Beta strandi207 – 21610
    Beta strandi221 – 2277
    Helixi229 – 24618
    Beta strandi249 – 2524
    Turni256 – 2583
    Helixi262 – 27413
    Helixi276 – 2816
    Helixi283 – 2886
    Helixi293 – 2953
    Helixi297 – 3037
    Helixi304 – 3063
    Helixi309 – 32517
    Beta strandi331 – 3333
    Turni334 – 3374
    Turni340 – 3423
    Beta strandi346 – 3483
    Helixi349 – 35810
    Turni359 – 3613
    Beta strandi362 – 3643
    Beta strandi368 – 3769
    Helixi380 – 39617
    Turni401 – 4033
    Beta strandi409 – 4113
    Turni414 – 4163
    Helixi418 – 4214
    Helixi423 – 4253
    Beta strandi426 – 4283
    Beta strandi430 – 43910
    Beta strandi444 – 4507
    Beta strandi455 – 4617
    Helixi463 – 48018
    Beta strandi484 – 4874
    Helixi493 – 50614
    Beta strandi516 – 5194
    Helixi521 – 53313
    Beta strandi539 – 5424
    Helixi544 – 55916
    Beta strandi562 – 57110
    Beta strandi576 – 5805
    Helixi587 – 59610
    Helixi604 – 62017
    Helixi624 – 64219
    Beta strandi649 – 6535
    Helixi656 – 67318
    Helixi678 – 69316
    Helixi695 – 7039
    Beta strandi706 – 7083
    Beta strandi715 – 7173
    Helixi720 – 7278
    Helixi731 – 7366
    Turni737 – 7393

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ITWX-ray1.95A/B/C/D1-741[»]
    1J1WX-ray3.20A/B/C/D1-741[»]
    ProteinModelPortaliP16100.
    SMRiP16100. Positions 2-741.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP16100.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni132 – 1398Substrate binding

    Domaini

    This molecule consists of two distinct domains, a small domain and a large domain. The structure of the large domain repeats a motif observed in the dimeric IDH. Such a fusional structure by domain duplication enables a single polypeptide chain to form a structure at the catalytic site that is homologous to the dimeric IDH, the catalytic site of which is located at the interface of two identical subunits.

    Sequence similaritiesi

    Belongs to the monomeric-type IDH family.Curated

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P16100-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTPKIIYTL TDEAPALATY SLLPIIKAFT GSSGIAVETR DISLAGRLIA    50
    TFPEYLTDTQ KISDDLAELG KLATTPDANI IKLPNISASV PQLKAAIKEL 100
    QQQGYKLPDY PEEPKTDTEK DVKARYDKIK GSAVNPVLRE GNSDRRAPLS 150
    VKNYARKHPH KMGAWSADSK SHVAHMDNGD FYGSEKAALI GAPGSVKIEL 200
    IAKDGSSTVL KAKTSVQAGE IIDSSVMSKN ALRNFIAAEI EDAKKQGVLL 250
    SVHLKATMMK VSDPIMFGQI VSEFYKDALT KHAEVLKQIG FDVNNGIGDL 300
    YARIKTLPEA KQKEIEADIQ AVYAQRPQLA MVNSDKGITN LHVPSDVIVD 350
    ASMPAMIRDS GKMWGPDGKL HDTKAVIPDR CYAGVYQVVI EDCKQHGAFD 400
    PTTMGSVPNV GLMAQKAEEY GSHDKTFQIP ADGVVRVTDE SGKLLLEQSV 450
    EAGDIWRMCQ AKDAPIQDWV KLAVNRARAT NTPAVFWLDP ARAHDAQVIA 500
    KVERYLKDYD TSGLDIRILS PVEATRFSLA RIREGKDTIS VTGNVLRDYL 550
    TDLFPIMELG TSAKMLSIVP LMSGGGLFET GAGGSAPKHV QQFLEEGYLR 600
    WDSLGEFLAL AASLEHLGNA YKNPKALVLA STLDQATGKI LDNNKSPARK 650
    VGEIDNRGSH FYLALYWAQA LAAQTEDKEL QAQFTGIAKA LTDNETKIVG 700
    ELAAAQGKPV DIAGYYHPNT DLTSKAIRPS ATFNAALAPL A 741
    Length:741
    Mass (Da):80,390
    Last modified:January 23, 2007 - v5
    Checksum:i29FF35278E5AED8B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D73443 Genomic DNA. Translation: BAA11169.1.
    PIRiA10759.
    JC7822.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D73443 Genomic DNA. Translation: BAA11169.1 .
    PIRi A10759.
    JC7822.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1ITW X-ray 1.95 A/B/C/D 1-741 [» ]
    1J1W X-ray 3.20 A/B/C/D 1-741 [» ]
    ProteinModelPortali P16100.
    SMRi P16100. Positions 2-741.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi P16100.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-13167.

    Miscellaneous databases

    EvolutionaryTracei P16100.

    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, sequencing, and expression of a gene encoding the monomeric isocitrate dehydrogenase of the nitrogen-fixing bacterium, Azotobacter vinelandii."
      Sahara T., Takada Y., Takeuchi Y., Yamaoka N., Fukunaga N.
      Biosci. Biotechnol. Biochem. 66:489-500(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-16.
    2. "Triphosphopyridine nucleotide specific isocitrate dehydrogenase from Azotobacter vinelandii. Alkylation of a specific methionine residue and amino acid sequence of the peptide containing this residue."
      Edwards D.J., Heinrikson R.L., Chung A.E.
      Biochemistry 13:677-683(1974) [PubMed] [Europe PMC] [Abstract]
      Cited for: PRELIMINARY PROTEIN SEQUENCE OF 229-251 AND 255-260.
    3. "Structure of the monomeric isocitrate dehydrogenase: evidence of a protein monomerization by a domain duplication."
      Yasutake Y., Watanabe S., Yao M., Takada Y., Fukunaga N., Tanaka I.
      Structure 10:1637-1648(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF COMPLEXES WITH ISOCITRATE; MANGANESE AND NADP, SUBUNIT.

    Entry informationi

    Entry nameiIDH_AZOVI
    AccessioniPrimary (citable) accession number: P16100
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 97 of the entry and version 5 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    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