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Protein

6-phosphogluconate dehydrogenase, decarboxylating 1

Gene

GND1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.1 Publication

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.1 Publication

Kineticsi

  1. KM=50 µM for 6-phosphogluconate1 Publication
  2. KM=35 µM for NADP1 Publication

    Pathwayi: pentose phosphate pathway

    This protein is involved in step 3 of the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage).
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. Glucose-6-phosphate 1-dehydrogenase (ZWF1)
    2. 6-phosphogluconolactonase 3 (SOL3), 6-phosphogluconolactonase 4 (SOL4)
    3. 6-phosphogluconate dehydrogenase, decarboxylating 2 (GND2), 6-phosphogluconate dehydrogenase, decarboxylating 1 (GND1)
    This subpathway is part of the pathway pentose phosphate pathway, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage), the pathway pentose phosphate pathway and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei102NADPBy similarity1
    Binding sitei102SubstrateBy similarity1
    Active sitei182Proton acceptorBy similarity1
    Active sitei189Proton donorBy similarity1
    Binding sitei190SubstrateBy similarity1
    Binding sitei259Substrate; via amide nitrogenBy similarity1
    Binding sitei286SubstrateBy similarity1
    Binding sitei446Substrate; shared with dimeric partnerBy similarity1
    Binding sitei452Substrate; shared with dimeric partnerBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi9 – 14NADPBy similarity6
    Nucleotide bindingi32 – 34NADPBy similarity3
    Nucleotide bindingi74 – 76NADPBy similarity3

    GO - Molecular functioni

    • phosphogluconate dehydrogenase (decarboxylating) activity Source: SGD

    GO - Biological processi

    • cellular response to oxidative stress Source: SGD
    • D-gluconate metabolic process Source: UniProtKB-KW
    • pentose-phosphate shunt, oxidative branch Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Gluconate utilization, Pentose shunt

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciYEAST:YHR183W-MONOMER.
    BRENDAi1.1.1.44. 984.
    ReactomeiR-SCE-71336. Pentose phosphate pathway (hexose monophosphate shunt).
    SABIO-RKP38720.
    UniPathwayiUPA00115; UER00410.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    6-phosphogluconate dehydrogenase, decarboxylating 1 (EC:1.1.1.44)
    Gene namesi
    Name:GND1
    Ordered Locus Names:YHR183W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome VIII

    Organism-specific databases

    EuPathDBiFungiDB:YHR183W.
    SGDiS000001226. GND1.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000900751 – 4896-phosphogluconate dehydrogenase, decarboxylating 1Add BLAST489

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei50PhosphoserineCombined sources1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP38720.
    PRIDEiP38720.
    TopDownProteomicsiP38720.

    PTM databases

    iPTMnetiP38720.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi36616. 144 interactors.
    DIPiDIP-6604N.
    IntActiP38720. 109 interactors.
    MINTiMINT-688249.

    Structurei

    Secondary structure

    1489
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 8Combined sources5
    Helixi12 – 23Combined sources12
    Beta strandi28 – 31Combined sources4
    Beta strandi33 – 35Combined sources3
    Helixi36 – 43Combined sources8
    Turni44 – 48Combined sources5
    Beta strandi49 – 52Combined sources4
    Helixi57 – 62Combined sources6
    Beta strandi69 – 72Combined sources4
    Helixi78 – 87Combined sources10
    Helixi88 – 90Combined sources3
    Beta strandi96 – 99Combined sources4
    Helixi105 – 117Combined sources13
    Beta strandi121 – 129Combined sources9
    Helixi130 – 136Combined sources7
    Beta strandi139 – 144Combined sources6
    Helixi146 – 148Combined sources3
    Helixi149 – 159Combined sources11
    Beta strandi166 – 168Combined sources3
    Helixi177 – 205Combined sources29
    Helixi211 – 222Combined sources12
    Turni223 – 226Combined sources4
    Helixi229 – 238Combined sources10
    Beta strandi245 – 247Combined sources3
    Helixi248 – 251Combined sources4
    Helixi261 – 272Combined sources12
    Helixi277 – 290Combined sources14
    Helixi292 – 301Combined sources10
    Helixi315 – 348Combined sources34
    Helixi354 – 362Combined sources9
    Beta strandi363 – 365Combined sources3
    Helixi370 – 381Combined sources12
    Helixi388 – 390Combined sources3
    Helixi392 – 415Combined sources24
    Helixi420 – 432Combined sources13
    Helixi439 – 449Combined sources11
    Helixi458 – 460Combined sources3
    Beta strandi463 – 465Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2P4QX-ray2.37A1-489[»]
    ProteinModelPortaliP38720.
    SMRiP38720.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP38720.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni128 – 130Substrate bindingBy similarity3
    Regioni185 – 186Substrate bindingBy similarity2

    Sequence similaritiesi

    Phylogenomic databases

    GeneTreeiENSGT00390000009023.
    HOGENOMiHOG000255147.
    InParanoidiP38720.
    KOiK00033.
    OMAiPQKEPFK.
    OrthoDBiEOG092C1NQM.

    Family and domain databases

    Gene3Di1.10.1040.10. 1 hit.
    1.20.5.320. 1 hit.
    3.40.50.720. 1 hit.
    InterProiIPR008927. 6-PGluconate_DH_C-like.
    IPR013328. 6PGD_dom_2.
    IPR012284. 6PGD_dom_3.
    IPR006114. 6PGDH_C.
    IPR006113. 6PGDH_Gnd/GntZ.
    IPR006115. 6PGDH_NADP-bd.
    IPR006184. 6PGdom_BS.
    IPR016040. NAD(P)-bd_dom.
    IPR006183. Pgluconate_DH.
    [Graphical view]
    PfamiPF00393. 6PGD. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000109. 6PGD. 1 hit.
    PRINTSiPR00076. 6PGDHDRGNASE.
    SMARTiSM01350. 6PGD. 1 hit.
    [Graphical view]
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR00873. gnd. 1 hit.
    PROSITEiPS00461. 6PGD. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P38720-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSADFGLIGL AVMGQNLILN AADHGFTVCA YNRTQSKVDH FLANEAKGKS
    60 70 80 90 100
    IIGATSIEDF ISKLKRPRKV MLLVKAGAPV DALINQIVPL LEKGDIIIDG
    110 120 130 140 150
    GNSHFPDSNR RYEELKKKGI LFVGSGVSGG EEGARYGPSL MPGGSEEAWP
    160 170 180 190 200
    HIKNIFQSIS AKSDGEPCCE WVGPAGAGHY VKMVHNGIEY GDMQLICEAY
    210 220 230 240 250
    DIMKRLGGFT DKEISDVFAK WNNGVLDSFL VEITRDILKF DDVDGKPLVE
    260 270 280 290 300
    KIMDTAGQKG TGKWTAINAL DLGMPVTLIG EAVFARCLSA LKNERIRASK
    310 320 330 340 350
    VLPGPEVPKD AVKDREQFVD DLEQALYASK IISYAQGFML IREAAATYGW
    360 370 380 390 400
    KLNNPAIALM WRGGCIIRSV FLGQITKAYR EEPDLENLLF NKFFADAVTK
    410 420 430 440 450
    AQSGWRKSIA LATTYGIPTP AFSTALSFYD GYRSERLPAN LLQAQRDYFG
    460 470 480
    AHTFRVLPEC ASDNLPVDKD IHINWTGHGG NVSSSTYQA
    Length:489
    Mass (Da):53,543
    Last modified:February 1, 1995 - v1
    Checksum:i55CAE5DACDC6A00B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z46631 Genomic DNA. Translation: CAA86600.1.
    U00028 Genomic DNA. Translation: AAB68452.1.
    U17155 Genomic DNA. Translation: AAA53637.1.
    BK006934 Genomic DNA. Translation: DAA06875.1.
    PIRiS46671.
    RefSeqiNP_012053.3. NM_001179314.3.

    Genome annotation databases

    EnsemblFungiiYHR183W; YHR183W; YHR183W.
    GeneIDi856589.
    KEGGisce:YHR183W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z46631 Genomic DNA. Translation: CAA86600.1.
    U00028 Genomic DNA. Translation: AAB68452.1.
    U17155 Genomic DNA. Translation: AAA53637.1.
    BK006934 Genomic DNA. Translation: DAA06875.1.
    PIRiS46671.
    RefSeqiNP_012053.3. NM_001179314.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2P4QX-ray2.37A1-489[»]
    ProteinModelPortaliP38720.
    SMRiP38720.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36616. 144 interactors.
    DIPiDIP-6604N.
    IntActiP38720. 109 interactors.
    MINTiMINT-688249.

    PTM databases

    iPTMnetiP38720.

    Proteomic databases

    MaxQBiP38720.
    PRIDEiP38720.
    TopDownProteomicsiP38720.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYHR183W; YHR183W; YHR183W.
    GeneIDi856589.
    KEGGisce:YHR183W.

    Organism-specific databases

    EuPathDBiFungiDB:YHR183W.
    SGDiS000001226. GND1.

    Phylogenomic databases

    GeneTreeiENSGT00390000009023.
    HOGENOMiHOG000255147.
    InParanoidiP38720.
    KOiK00033.
    OMAiPQKEPFK.
    OrthoDBiEOG092C1NQM.

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00410.
    BioCyciYEAST:YHR183W-MONOMER.
    BRENDAi1.1.1.44. 984.
    ReactomeiR-SCE-71336. Pentose phosphate pathway (hexose monophosphate shunt).
    SABIO-RKP38720.

    Miscellaneous databases

    EvolutionaryTraceiP38720.
    PROiP38720.

    Family and domain databases

    Gene3Di1.10.1040.10. 1 hit.
    1.20.5.320. 1 hit.
    3.40.50.720. 1 hit.
    InterProiIPR008927. 6-PGluconate_DH_C-like.
    IPR013328. 6PGD_dom_2.
    IPR012284. 6PGD_dom_3.
    IPR006114. 6PGDH_C.
    IPR006113. 6PGDH_Gnd/GntZ.
    IPR006115. 6PGDH_NADP-bd.
    IPR006184. 6PGdom_BS.
    IPR016040. NAD(P)-bd_dom.
    IPR006183. Pgluconate_DH.
    [Graphical view]
    PfamiPF00393. 6PGD. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000109. 6PGD. 1 hit.
    PRINTSiPR00076. 6PGDHDRGNASE.
    SMARTiSM01350. 6PGD. 1 hit.
    [Graphical view]
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR00873. gnd. 1 hit.
    PROSITEiPS00461. 6PGD. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry namei6PGD1_YEAST
    AccessioniPrimary (citable) accession number: P38720
    Secondary accession number(s): D3DLD1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: November 2, 2016
    This is version 155 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 101000 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome VIII
      Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.