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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Escherichia coli (strain K12)
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=49 µM for NADP1 Publication
  2. KM=93 µM for 6-phospho-D-gluconate1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei102 – 1021NADPBy similarity
    Binding sitei102 – 1021Substrate
    Active sitei183 – 1831Proton acceptor1 Publication
    Active sitei190 – 1901Proton donor1 Publication
    Binding sitei191 – 1911SubstrateBy similarity
    Binding sitei260 – 2601Substrate; via amide nitrogen
    Binding sitei287 – 2871Substrate
    Binding sitei445 – 4451Substrate; shared with dimeric partner
    Binding sitei451 – 4511Substrate; shared with dimeric partner

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi10 – 156NADP
    Nucleotide bindingi33 – 353NADP
    Nucleotide bindingi74 – 763NADP

    GO - Molecular functioni

    • identical protein binding Source: IntAct
    • NADP binding Source: InterPro
    • phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    • D-gluconate metabolic process Source: UniProtKB-KW
    • pentose-phosphate shunt Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Gluconate utilization, Pentose shunt

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:6PGLUCONDEHYDROG-MONOMER.
    ECOL316407:JW2011-MONOMER.
    MetaCyc:6PGLUCONDEHYDROG-MONOMER.
    BRENDAi1.1.1.44. 2026.
    UniPathwayiUPA00115; UER00410.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
    Gene namesi
    Name:gnd
    Ordered Locus Names:b2029, JW2011
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10411. gnd.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 4684686-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090037Add
    BLAST

    Proteomic databases

    PRIDEiP00350.

    Expressioni

    Gene expression databases

    GenevestigatoriP00350.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself4EBI-907049,EBI-907049

    Protein-protein interaction databases

    DIPiDIP-9819N.
    IntActiP00350. 5 interactions.

    Structurei

    Secondary structure

    1
    468
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 96Combined sources
    Helixi13 – 2311Combined sources
    Turni24 – 263Combined sources
    Beta strandi29 – 324Combined sources
    Helixi36 – 4510Combined sources
    Beta strandi51 – 533Combined sources
    Helixi57 – 626Combined sources
    Beta strandi69 – 724Combined sources
    Beta strandi76 – 783Combined sources
    Helixi79 – 879Combined sources
    Helixi88 – 903Combined sources
    Beta strandi96 – 994Combined sources
    Helixi105 – 11713Combined sources
    Beta strandi121 – 1299Combined sources
    Helixi130 – 1367Combined sources
    Beta strandi139 – 1446Combined sources
    Helixi146 – 15914Combined sources
    Beta strandi168 – 1703Combined sources
    Helixi178 – 20831Combined sources
    Helixi212 – 22413Combined sources
    Turni225 – 2273Combined sources
    Helixi230 – 24011Combined sources
    Beta strandi246 – 2483Combined sources
    Helixi249 – 2524Combined sources
    Helixi265 – 2739Combined sources
    Helixi278 – 29013Combined sources
    Helixi293 – 3008Combined sources
    Helixi314 – 34734Combined sources
    Helixi353 – 3597Combined sources
    Beta strandi361 – 3644Combined sources
    Helixi370 – 38011Combined sources
    Helixi387 – 3893Combined sources
    Helixi391 – 41424Combined sources
    Helixi419 – 43113Combined sources
    Helixi438 – 44912Combined sources
    Beta strandi455 – 4584Combined sources
    Beta strandi460 – 4623Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZYAX-ray1.60A/B1-468[»]
    2ZYDX-ray1.50A/B1-468[»]
    3FWNX-ray1.50A/B1-468[»]
    ProteinModelPortaliP00350.
    SMRiP00350. Positions 2-467.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00350.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni128 – 1303Substrate binding
    Regioni186 – 1872Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    InParanoidiP00350.
    KOiK00033.
    OMAiSDEYNWD.
    OrthoDBiEOG6MSS4W.
    PhylomeDBiP00350.

    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.

    P00350-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKQQIGVVG MAVMGRNLAL NIESRGYTVS IFNRSREKTE EVIAENPGKK
    60 70 80 90 100
    LVPYYTVKEF VESLETPRRI LLMVKAGAGT DAAIDSLKPY LDKGDIIIDG
    110 120 130 140 150
    GNTFFQDTIR RNRELSAEGF NFIGTGVSGG EEGALKGPSI MPGGQKEAYE
    160 170 180 190 200
    LVAPILTKIA AVAEDGEPCV TYIGADGAGH YVKMVHNGIE YGDMQLIAEA
    210 220 230 240 250
    YSLLKGGLNL TNEELAQTFT EWNNGELSSY LIDITKDIFT KKDEDGNYLV
    260 270 280 290 300
    DVILDEAANK GTGKWTSQSA LDLGEPLSLI TESVFARYIS SLKDQRVAAS
    310 320 330 340 350
    KVLSGPQAQP AGDKAEFIEK VRRALYLGKI VSYAQGFSQL RAASEEYNWD
    360 370 380 390 400
    LNYGEIAKIF RAGCIIRAQF LQKITDAYAE NPQIANLLLA PYFKQIADDY
    410 420 430 440 450
    QQALRDVVAY AVQNGIPVPT FSAAVAYYDS YRAAVLPANL IQAQRDYFGA
    460
    HTYKRIDKEG VFHTEWLD
    Length:468
    Mass (Da):51,481
    Last modified:November 1, 1997 - v2
    Checksum:i62A32C84DC596D86
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti306 – 3061P → R in AAA23918 (PubMed:6329905).Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti2 – 21S → L in strain: ECOR 70.
    Natural varianti32 – 321F → Y in strain: ECOR 70.
    Natural varianti39 – 391T → Q in strain: O7:K1 / VW187.
    Natural varianti52 – 521V → D in strain: ECOR 10.
    Natural varianti55 – 551Y → F in strain: ECOR 10.
    Natural varianti102 – 1021N → K in strain: ECOR 65.
    Natural varianti117 – 1171A → S in strain: ECOR 70.
    Natural varianti123 – 1253IGT → YRY in strain: O7:K1 / VW187.
    Natural varianti170 – 1701V → F in strain: ECOR 10.
    Natural varianti175 – 1751A → S in strain: ECOR 45.
    Natural varianti209 – 2091N → S in strain: ECOR 68.
    Natural varianti211 – 2111T → S in strain: ECOR 10 and ECOR 69.
    Natural varianti216 – 2161A → T in strain: ECOR 67.
    Natural varianti294 – 2941D → E in strain: ECOR 70.
    Natural varianti308 – 3081A → G in strain: ECOR 68.
    Natural varianti313 – 3131D → N in strain: ECOR 67.
    Natural varianti315 – 3151A → G in strain: ECOR 70.
    Natural varianti325 – 3251L → Q in strain: ECOR 69.
    Natural varianti330 – 3301I → S in strain: ECOR 10.
    Natural varianti350 – 3501D → A in strain: ECOR 10 and ECOR 69.
    Natural varianti369 – 3691Q → R in strain: ECOR 10.
    Natural varianti422 – 4221S → A in strain: ECOR 10, ECOR 65, ECOR 68, ECOR 69 and ECOR 70.

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    K02072 Genomic DNA. Translation: AAA23918.1.
    M63821 Genomic DNA. Translation: AAA24488.1.
    M64326 Genomic DNA. Translation: AAA24204.1.
    M64327 Genomic DNA. Translation: AAA24205.1.
    M64328 Genomic DNA. Translation: AAA24206.1.
    M64329 Genomic DNA. Translation: AAA24207.1.
    M64330 Genomic DNA. Translation: AAA24208.1.
    M64331 Genomic DNA. Translation: AAA24209.1.
    U00096 Genomic DNA. Translation: AAC75090.1.
    AP009048 Genomic DNA. Translation: BAA15869.1.
    M23181 Genomic DNA. Translation: AAA23924.1.
    M18956 Genomic DNA. Translation: AAA23919.1.
    M18957 Genomic DNA. Translation: AAA23920.1.
    M18960 Genomic DNA. Translation: AAA23922.1.
    AF125322 Genomic DNA. Translation: AAC27540.1.
    PIRiD64968. DEECGC.
    I62463.
    I62465.
    RefSeqiNP_416533.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC75090; AAC75090; b2029.
    BAA15869; BAA15869; BAA15869.
    GeneIDi946554.
    KEGGiecj:Y75_p1992.
    eco:b2029.
    PATRICi32119393. VBIEscCol129921_2106.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    K02072 Genomic DNA. Translation: AAA23918.1.
    M63821 Genomic DNA. Translation: AAA24488.1.
    M64326 Genomic DNA. Translation: AAA24204.1.
    M64327 Genomic DNA. Translation: AAA24205.1.
    M64328 Genomic DNA. Translation: AAA24206.1.
    M64329 Genomic DNA. Translation: AAA24207.1.
    M64330 Genomic DNA. Translation: AAA24208.1.
    M64331 Genomic DNA. Translation: AAA24209.1.
    U00096 Genomic DNA. Translation: AAC75090.1.
    AP009048 Genomic DNA. Translation: BAA15869.1.
    M23181 Genomic DNA. Translation: AAA23924.1.
    M18956 Genomic DNA. Translation: AAA23919.1.
    M18957 Genomic DNA. Translation: AAA23920.1.
    M18960 Genomic DNA. Translation: AAA23922.1.
    AF125322 Genomic DNA. Translation: AAC27540.1.
    PIRiD64968. DEECGC.
    I62463.
    I62465.
    RefSeqiNP_416533.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZYAX-ray1.60A/B1-468[»]
    2ZYDX-ray1.50A/B1-468[»]
    3FWNX-ray1.50A/B1-468[»]
    ProteinModelPortaliP00350.
    SMRiP00350. Positions 2-467.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-9819N.
    IntActiP00350. 5 interactions.

    Proteomic databases

    PRIDEiP00350.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75090; AAC75090; b2029.
    BAA15869; BAA15869; BAA15869.
    GeneIDi946554.
    KEGGiecj:Y75_p1992.
    eco:b2029.
    PATRICi32119393. VBIEscCol129921_2106.

    Organism-specific databases

    EchoBASEiEB0406.
    EcoGeneiEG10411. gnd.

    Phylogenomic databases

    InParanoidiP00350.
    KOiK00033.
    OMAiSDEYNWD.
    OrthoDBiEOG6MSS4W.
    PhylomeDBiP00350.

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00410.
    BioCyciEcoCyc:6PGLUCONDEHYDROG-MONOMER.
    ECOL316407:JW2011-MONOMER.
    MetaCyc:6PGLUCONDEHYDROG-MONOMER.
    BRENDAi1.1.1.44. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP00350.
    PROiP00350.

    Gene expression databases

    GenevestigatoriP00350.

    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. "DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase."
      Nasoff M.S., Baker H.V. II, Wolf R.E. Jr.
      Gene 27:253-264(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus."
      Bisercic M., Feutrier J.Y., Reeves P.R.
      J. Bacteriol. 173:3894-3900(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ECOR 10.
    3. "Recombination in Escherichia coli and the definition of biological species."
      Dykhuizen D.E., Green L.
      J. Bacteriol. 173:7257-7268(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ECOR 45, ECOR 65, ECOR 67, ECOR 68, ECOR 69 and ECOR 70.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. "Fitness effects of a deletion mutation increasing transcription of the 6-phosphogluconate dehydrogenase gene in Escherichia coli."
      Miller R.D., Dykhuizen D.E., Hartl D.L.
      Mol. Biol. Evol. 5:691-703(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
    8. "Comparative nucleotide sequence analysis of growth-rate-regulated gnd alleles from natural isolates of Escherichia coli and from Salmonella typhimurium LT-2."
      Barcak G.J., Wolf R.E. Jr.
      J. Bacteriol. 170:372-379(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
    9. "Identification, expression, and DNA sequence of the GDP-mannose biosynthesis genes encoded by the O7 rfb gene cluster of strain VW187 (Escherichia coli O7:K1)."
      Marolda C.L., Valvano M.A.
      J. Bacteriol. 175:148-158(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
      Strain: O7:K1 / VW187.
    10. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    11. "Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism."
      Chen Y.Y., Ko T.P., Chen W.H., Lo L.P., Lin C.H., Wang A.H.
      J. Struct. Biol. 169:25-35(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEXES WITH NADP AND SUBSTRATE, SUBUNIT, CATALYTIC ACTIVITY, FUNCTION, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry namei6PGD_ECOLI
    AccessioniPrimary (citable) accession number: P00350
    Secondary accession number(s): P78080
    , Q47571, Q59366, Q59402, Q59411, Q59412, Q59413, Q59414, Q59416, Q79DT3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: November 1, 1997
    Last modified: May 27, 2015
    This is version 134 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    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.