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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

    Pathway:ipentose 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei102 – 1021NADPBy similarity
    Binding sitei102 – 1021SubstrateBy similarity
    Active sitei182 – 1821Proton acceptorBy similarity
    Active sitei189 – 1891Proton donorBy similarity
    Binding sitei190 – 1901SubstrateBy similarity
    Binding sitei259 – 2591Substrate; via amide nitrogenBy similarity
    Binding sitei286 – 2861SubstrateBy similarity
    Binding sitei446 – 4461Substrate; shared with dimeric partnerBy similarity
    Binding sitei452 – 4521Substrate; shared with dimeric partnerBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi9 – 146NADPBy similarity
    Nucleotide bindingi32 – 343NADPBy similarity
    Nucleotide bindingi74 – 763NADPBy similarity

    GO - Molecular functioni

    • NADP binding Source: InterPro
    • 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.
    ReactomeiREACT_318870. 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
    ProteomesiUP000002311 Componenti: Chromosome VIII

    Organism-specific databases

    CYGDiYHR183w.
    EuPathDBiFungiDB:YHR183W.
    SGDiS000001226. GND1.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 4894896-phosphogluconate dehydrogenase, decarboxylating 1PRO_0000090075Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei50 – 501Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP38720.
    PaxDbiP38720.
    PeptideAtlasiP38720.
    PRIDEiP38720.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi36616. 142 interactions.
    DIPiDIP-6604N.
    IntActiP38720. 109 interactions.
    MINTiMINT-688249.

    Structurei

    Secondary structure

    1
    489
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 85Combined sources
    Helixi12 – 2312Combined sources
    Beta strandi28 – 314Combined sources
    Beta strandi33 – 353Combined sources
    Helixi36 – 438Combined sources
    Turni44 – 485Combined sources
    Beta strandi49 – 524Combined sources
    Helixi57 – 626Combined sources
    Beta strandi69 – 724Combined sources
    Helixi78 – 8710Combined sources
    Helixi88 – 903Combined sources
    Beta strandi96 – 994Combined sources
    Helixi105 – 11713Combined sources
    Beta strandi121 – 1299Combined sources
    Helixi130 – 1367Combined sources
    Beta strandi139 – 1446Combined sources
    Helixi146 – 1483Combined sources
    Helixi149 – 15911Combined sources
    Beta strandi166 – 1683Combined sources
    Helixi177 – 20529Combined sources
    Helixi211 – 22212Combined sources
    Turni223 – 2264Combined sources
    Helixi229 – 23810Combined sources
    Beta strandi245 – 2473Combined sources
    Helixi248 – 2514Combined sources
    Helixi261 – 27212Combined sources
    Helixi277 – 29014Combined sources
    Helixi292 – 30110Combined sources
    Helixi315 – 34834Combined sources
    Helixi354 – 3629Combined sources
    Beta strandi363 – 3653Combined sources
    Helixi370 – 38112Combined sources
    Helixi388 – 3903Combined sources
    Helixi392 – 41524Combined sources
    Helixi420 – 43213Combined sources
    Helixi439 – 44911Combined sources
    Helixi458 – 4603Combined sources
    Beta strandi463 – 4653Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2P4QX-ray2.37A1-489[»]
    ProteinModelPortaliP38720.
    SMRiP38720. Positions 1-476.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP38720.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni128 – 1303Substrate bindingBy similarity
    Regioni185 – 1862Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0362.
    GeneTreeiENSGT00390000009023.
    HOGENOMiHOG000255147.
    InParanoidiP38720.
    KOiK00033.
    OMAiLGGFTDK.
    OrthoDBiEOG7F252Z.

    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.
    SUPFAMiSSF48179. SSF48179. 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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2P4QX-ray2.37A1-489[»]
    ProteinModelPortaliP38720.
    SMRiP38720. Positions 1-476.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36616. 142 interactions.
    DIPiDIP-6604N.
    IntActiP38720. 109 interactions.
    MINTiMINT-688249.

    Proteomic databases

    MaxQBiP38720.
    PaxDbiP38720.
    PeptideAtlasiP38720.
    PRIDEiP38720.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    CYGDiYHR183w.
    EuPathDBiFungiDB:YHR183W.
    SGDiS000001226. GND1.

    Phylogenomic databases

    eggNOGiCOG0362.
    GeneTreeiENSGT00390000009023.
    HOGENOMiHOG000255147.
    InParanoidiP38720.
    KOiK00033.
    OMAiLGGFTDK.
    OrthoDBiEOG7F252Z.

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00410.
    BioCyciYEAST:YHR183W-MONOMER.
    BRENDAi1.1.1.44. 984.
    ReactomeiREACT_318870. Pentose phosphate pathway (hexose monophosphate shunt).
    SABIO-RKP38720.

    Miscellaneous databases

    EvolutionaryTraceiP38720.
    NextBioi982464.
    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.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    TIGRFAMsiTIGR00873. gnd. 1 hit.
    PROSITEiPS00461. 6PGD. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Desouza M., Lobo Z., Maitra P.K.
      Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: PROTEIN SEQUENCE OF 41-47 AND 120-131.
      Strain: ATCC 204508 / S288c.
    5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1."
      He W., Wang Y., Liu W., Zhou C.Z.
      BMC Struct. Biol. 7:38-38(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) IN COMPLEX WITH CITRATE, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.

    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: July 22, 2015
    This is version 143 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

    External Data

    Dasty 3

    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 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.