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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: 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).1 Publication
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. Glucose-6-phosphate 1-dehydrogenase (zwf)
    2. 6-phosphogluconolactonase (pgl)
    3. 6-phosphogluconate dehydrogenase, decarboxylating (gnd)
    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 sitei102Substrate1
    Active sitei183Proton acceptor1 Publication1
    Active sitei190Proton donor1 Publication1
    Binding sitei191SubstrateBy similarity1
    Binding sitei260Substrate; via amide nitrogen1
    Binding sitei287Substrate1
    Binding sitei445Substrate; shared with dimeric partner1
    Binding sitei451Substrate; shared with dimeric partner1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi10 – 15NADP6
    Nucleotide bindingi33 – 35NADP3
    Nucleotide bindingi74 – 76NADP3

    GO - Molecular functioni

    • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10411. gnd.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000900371 – 4686-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST468

    Proteomic databases

    EPDiP00350.
    PaxDbiP00350.
    PRIDEiP00350.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

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

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Protein-protein interaction databases

    BioGridi4261354. 7 interactors.
    DIPiDIP-9819N.
    IntActiP00350. 5 interactors.
    STRINGi511145.b2029.

    Structurei

    Secondary structure

    1468
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 9Combined sources6
    Helixi13 – 23Combined sources11
    Turni24 – 26Combined sources3
    Beta strandi29 – 32Combined sources4
    Helixi36 – 45Combined sources10
    Beta strandi51 – 53Combined sources3
    Helixi57 – 62Combined sources6
    Beta strandi69 – 72Combined sources4
    Beta strandi76 – 78Combined sources3
    Helixi79 – 87Combined sources9
    Helixi88 – 90Combined sources3
    Beta strandi96 – 99Combined sources4
    Helixi105 – 117Combined sources13
    Beta strandi121 – 129Combined sources9
    Helixi130 – 136Combined sources7
    Beta strandi139 – 144Combined sources6
    Helixi146 – 159Combined sources14
    Beta strandi168 – 170Combined sources3
    Helixi178 – 208Combined sources31
    Helixi212 – 224Combined sources13
    Turni225 – 227Combined sources3
    Helixi230 – 240Combined sources11
    Beta strandi246 – 248Combined sources3
    Helixi249 – 252Combined sources4
    Helixi265 – 273Combined sources9
    Helixi278 – 290Combined sources13
    Helixi293 – 300Combined sources8
    Helixi314 – 347Combined sources34
    Helixi353 – 359Combined sources7
    Beta strandi361 – 364Combined sources4
    Helixi370 – 380Combined sources11
    Helixi387 – 389Combined sources3
    Helixi391 – 414Combined sources24
    Helixi419 – 431Combined sources13
    Helixi438 – 449Combined sources12
    Beta strandi455 – 458Combined sources4
    Beta strandi460 – 462Combined sources3

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP00350.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni128 – 130Substrate binding3
    Regioni186 – 187Substrate bindingBy similarity2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C7Q. Bacteria.
    COG0362. LUCA.
    InParanoidiP00350.
    KOiK00033.
    OMAiEGEPCVT.
    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.
    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.

    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)DescriptionActionsGraphical viewLength
    Sequence conflicti306P → R in AAA23918 (PubMed:6329905).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural varianti2S → L in strain: ECOR 70. 1
    Natural varianti32F → Y in strain: ECOR 70. 1
    Natural varianti39T → Q in strain: O7:K1 / VW187. 1
    Natural varianti52V → D in strain: ECOR 10. 1
    Natural varianti55Y → F in strain: ECOR 10. 1
    Natural varianti102N → K in strain: ECOR 65. 1
    Natural varianti117A → S in strain: ECOR 70. 1
    Natural varianti123 – 125IGT → YRY in strain: O7:K1 / VW187. 3
    Natural varianti170V → F in strain: ECOR 10. 1
    Natural varianti175A → S in strain: ECOR 45. 1
    Natural varianti209N → S in strain: ECOR 68. 1
    Natural varianti211T → S in strain: ECOR 10 and ECOR 69. 1
    Natural varianti216A → T in strain: ECOR 67. 1
    Natural varianti294D → E in strain: ECOR 70. 1
    Natural varianti308A → G in strain: ECOR 68. 1
    Natural varianti313D → N in strain: ECOR 67. 1
    Natural varianti315A → G in strain: ECOR 70. 1
    Natural varianti325L → Q in strain: ECOR 69. 1
    Natural varianti330I → S in strain: ECOR 10. 1
    Natural varianti350D → A in strain: ECOR 10 and ECOR 69. 1
    Natural varianti369Q → R in strain: ECOR 10. 1
    Natural varianti422S → A in strain: ECOR 10, ECOR 65, ECOR 68, ECOR 69 and ECOR 70. 1

    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.
    WP_000043484.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75090; AAC75090; b2029.
    BAA15869; BAA15869; BAA15869.
    GeneIDi946554.
    KEGGiecj:JW2011.
    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.
    WP_000043484.1. NZ_LN832404.1.

    3D structure databases

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

    Protein-protein interaction databases

    BioGridi4261354. 7 interactors.
    DIPiDIP-9819N.
    IntActiP00350. 5 interactors.
    STRINGi511145.b2029.

    Proteomic databases

    EPDiP00350.
    PaxDbiP00350.
    PRIDEiP00350.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75090; AAC75090; b2029.
    BAA15869; BAA15869; BAA15869.
    GeneIDi946554.
    KEGGiecj:JW2011.
    eco:b2029.
    PATRICi32119393. VBIEscCol129921_2106.

    Organism-specific databases

    EchoBASEiEB0406.
    EcoGeneiEG10411. gnd.

    Phylogenomic databases

    eggNOGiENOG4105C7Q. Bacteria.
    COG0362. LUCA.
    InParanoidiP00350.
    KOiK00033.
    OMAiEGEPCVT.
    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.

    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 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: November 2, 2016
    This is version 147 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

    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.