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P00350

- 6PGD_ECOLI

UniProt

P00350 - 6PGD_ECOLI

Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 128 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      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=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

    1. identical protein binding Source: IntAct
    2. NADP binding Source: InterPro
    3. phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB
    4. protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    1. D-gluconate metabolic process Source: UniProtKB-KW
    2. pentose-phosphate shunt Source: UniProtKB

    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.
    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: Chromosome, UP000000625: 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 – 96
    Helixi13 – 2311
    Turni24 – 263
    Beta strandi29 – 324
    Helixi36 – 4510
    Beta strandi51 – 533
    Helixi57 – 626
    Beta strandi69 – 724
    Beta strandi76 – 783
    Helixi79 – 879
    Helixi88 – 903
    Beta strandi96 – 994
    Helixi105 – 11713
    Beta strandi121 – 1299
    Helixi130 – 1367
    Beta strandi139 – 1446
    Helixi146 – 15914
    Beta strandi168 – 1703
    Helixi178 – 20831
    Helixi212 – 22413
    Turni225 – 2273
    Helixi230 – 24011
    Beta strandi246 – 2483
    Helixi249 – 2524
    Helixi265 – 2739
    Helixi278 – 29013
    Helixi293 – 3008
    Helixi314 – 34734
    Helixi353 – 3597
    Beta strandi361 – 3644
    Helixi370 – 38011
    Helixi387 – 3893
    Helixi391 – 41424
    Helixi419 – 43113
    Helixi438 – 44912
    Beta strandi455 – 4584
    Beta strandi460 – 4623

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZYAX-ray1.60A/B1-468[»]
    2ZYDX-ray1.50A/B1-468[»]
    3FWNX-ray1.50A/B1-468[»]
    ProteinModelPortaliP00350.
    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

    KOiK00033.
    OMAiDKDGVFH.
    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.
    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.

    P00350-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKQQIGVVG MAVMGRNLAL NIESRGYTVS IFNRSREKTE EVIAENPGKK    50
    LVPYYTVKEF VESLETPRRI LLMVKAGAGT DAAIDSLKPY LDKGDIIIDG 100
    GNTFFQDTIR RNRELSAEGF NFIGTGVSGG EEGALKGPSI MPGGQKEAYE 150
    LVAPILTKIA AVAEDGEPCV TYIGADGAGH YVKMVHNGIE YGDMQLIAEA 200
    YSLLKGGLNL TNEELAQTFT EWNNGELSSY LIDITKDIFT KKDEDGNYLV 250
    DVILDEAANK GTGKWTSQSA LDLGEPLSLI TESVFARYIS SLKDQRVAAS 300
    KVLSGPQAQP AGDKAEFIEK VRRALYLGKI VSYAQGFSQL RAASEEYNWD 350
    LNYGEIAKIF RAGCIIRAQF LQKITDAYAE NPQIANLLLA PYFKQIADDY 400
    QQALRDVVAY AVQNGIPVPT FSAAVAYYDS YRAAVLPANL IQAQRDYFGA 450
    HTYKRIDKEG VFHTEWLD 468
    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:
    EMBL
    GenBank
    DDBJ
    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.
    YP_490272.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75090; AAC75090; b2029.
    BAA15869; BAA15869; BAA15869.
    GeneIDi12932360.
    946554.
    KEGGiecj:Y75_p1992.
    eco:b2029.
    PATRICi32119393. VBIEscCol129921_2106.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi D64968. DEECGC.
    I62463.
    I62465.
    RefSeqi NP_416533.1. NC_000913.3.
    YP_490272.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2ZYA X-ray 1.60 A/B 1-468 [» ]
    2ZYD X-ray 1.50 A/B 1-468 [» ]
    3FWN X-ray 1.50 A/B 1-468 [» ]
    ProteinModelPortali P00350.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9819N.
    IntActi P00350. 5 interactions.

    Proteomic databases

    PRIDEi P00350.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75090 ; AAC75090 ; b2029 .
    BAA15869 ; BAA15869 ; BAA15869 .
    GeneIDi 12932360.
    946554.
    KEGGi ecj:Y75_p1992.
    eco:b2029.
    PATRICi 32119393. VBIEscCol129921_2106.

    Organism-specific databases

    EchoBASEi EB0406.
    EcoGenei EG10411. gnd.

    Phylogenomic databases

    KOi K00033.
    OMAi DKDGVFH.
    OrthoDBi EOG6MSS4W.
    PhylomeDBi P00350.

    Enzyme and pathway databases

    UniPathwayi UPA00115 ; UER00410 .
    BioCyci EcoCyc:6PGLUCONDEHYDROG-MONOMER.
    ECOL316407:JW2011-MONOMER.
    MetaCyc:6PGLUCONDEHYDROG-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P00350.
    PROi P00350.

    Gene expression databases

    Genevestigatori P00350.

    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. "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: October 1, 2014
    This is version 128 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