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P38720

- 6PGD1_YEAST

UniProt

P38720 - 6PGD1_YEAST

Protein

6-phosphogluconate dehydrogenase, decarboxylating 1

Gene

GND1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 135 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    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

    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

    1. NADP binding Source: InterPro
    2. phosphogluconate dehydrogenase (decarboxylating) activity Source: SGD

    GO - Biological processi

    1. cellular response to oxidative stress Source: SGD
    2. D-gluconate metabolic process Source: UniProtKB-KW
    3. pentose-phosphate shunt, oxidative branch Source: SGD

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Gluconate utilization, Pentose shunt

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciYEAST:YHR183W-MONOMER.
    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: Chromosome VIII

    Organism-specific databases

    CYGDiYHR183w.
    SGDiS000001226. GND1.

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    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.

    Expressioni

    Gene expression databases

    GenevestigatoriP38720.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi36616. 142 interactions.
    DIPiDIP-6604N.
    IntActiP38720. 109 interactions.
    MINTiMINT-688249.
    STRINGi4932.YHR183W.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK00033.
    OMAiEFNWNLP.
    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.
    IPR006114. 6PGDH_C.
    IPR006113. 6PGDH_decarbox.
    IPR006115. 6PGDH_NADP-bd.
    IPR006184. 6PGdom_BS.
    IPR013328. DH_multihelical.
    IPR012284. Fibritin/6PGD_C-extension.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00393. 6PGD. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000109. 6PGD. 1 hit.
    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

    MSADFGLIGL AVMGQNLILN AADHGFTVCA YNRTQSKVDH FLANEAKGKS    50
    IIGATSIEDF ISKLKRPRKV MLLVKAGAPV DALINQIVPL LEKGDIIIDG 100
    GNSHFPDSNR RYEELKKKGI LFVGSGVSGG EEGARYGPSL MPGGSEEAWP 150
    HIKNIFQSIS AKSDGEPCCE WVGPAGAGHY VKMVHNGIEY GDMQLICEAY 200
    DIMKRLGGFT DKEISDVFAK WNNGVLDSFL VEITRDILKF DDVDGKPLVE 250
    KIMDTAGQKG TGKWTAINAL DLGMPVTLIG EAVFARCLSA LKNERIRASK 300
    VLPGPEVPKD AVKDREQFVD DLEQALYASK IISYAQGFML IREAAATYGW 350
    KLNNPAIALM WRGGCIIRSV FLGQITKAYR EEPDLENLLF NKFFADAVTK 400
    AQSGWRKSIA LATTYGIPTP AFSTALSFYD GYRSERLPAN LLQAQRDYFG 450
    AHTFRVLPEC ASDNLPVDKD IHINWTGHGG NVSSSTYQA 489
    Length:489
    Mass (Da):53,543
    Last modified:February 1, 1995 - v1
    Checksum:i55CAE5DACDC6A00B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi S46671.
    RefSeqi NP_012053.3. NM_001179314.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2P4Q X-ray 2.37 A 1-489 [» ]
    ProteinModelPortali P38720.
    SMRi P38720. Positions 1-476.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36616. 142 interactions.
    DIPi DIP-6604N.
    IntActi P38720. 109 interactions.
    MINTi MINT-688249.
    STRINGi 4932.YHR183W.

    Proteomic databases

    MaxQBi P38720.
    PaxDbi P38720.
    PeptideAtlasi P38720.
    PRIDEi P38720.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YHR183W ; YHR183W ; YHR183W .
    GeneIDi 856589.
    KEGGi sce:YHR183W.

    Organism-specific databases

    CYGDi YHR183w.
    SGDi S000001226. GND1.

    Phylogenomic databases

    eggNOGi COG0362.
    GeneTreei ENSGT00390000009023.
    HOGENOMi HOG000255147.
    KOi K00033.
    OMAi EFNWNLP.
    OrthoDBi EOG7F252Z.

    Enzyme and pathway databases

    UniPathwayi UPA00115 ; UER00410 .
    BioCyci YEAST:YHR183W-MONOMER.
    SABIO-RK P38720.

    Miscellaneous databases

    EvolutionaryTracei P38720.
    NextBioi 982464.

    Gene expression databases

    Genevestigatori P38720.

    Family and domain databases

    Gene3Di 1.10.1040.10. 1 hit.
    1.20.5.320. 1 hit.
    3.40.50.720. 1 hit.
    InterProi IPR008927. 6-PGluconate_DH_C-like.
    IPR006114. 6PGDH_C.
    IPR006113. 6PGDH_decarbox.
    IPR006115. 6PGDH_NADP-bd.
    IPR006184. 6PGdom_BS.
    IPR013328. DH_multihelical.
    IPR012284. Fibritin/6PGD_C-extension.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    Pfami PF00393. 6PGD. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000109. 6PGD. 1 hit.
    SUPFAMi SSF48179. SSF48179. 1 hit.
    TIGRFAMsi TIGR00873. gnd. 1 hit.
    PROSITEi PS00461. 6PGD. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 135 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