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Protein

6-phosphogluconate dehydrogenase, decarboxylating 2, chloroplastic

Gene

pgdP

Organism
Spinacia oleracea (Spinach)
Status
Reviewed-Annotation score: Annotation score: 4 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.

Kineticsi

  1. KM=40 µM for 6-phosphoglutanate1 Publication
  2. KM=6 µM for NADP1 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).
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase, chloroplastic (G6PD), Glucose-6-phosphate 1-dehydrogenase (SOVF_162250), Glucose-6-phosphate 1-dehydrogenase (SOVF_004890), Glucose-6-phosphate 1-dehydrogenase (SOVF_183760)
    2. no protein annotated in this organism
    3. 6-phosphogluconate dehydrogenase, decarboxylating 2, chloroplastic (pgdP), 6-phosphogluconate dehydrogenase, decarboxylating (SOVF_090000), 6-phosphogluconate dehydrogenase, decarboxylating (SOVF_128490), 6-phosphogluconate dehydrogenase, decarboxylating 1 (pgdC)
    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 sitei150NADPBy similarity1
    Binding sitei150SubstrateBy similarity1
    Active sitei230Proton acceptorBy similarity1
    Active sitei237Proton donorBy similarity1
    Binding sitei238SubstrateBy similarity1
    Binding sitei308Substrate; via amide nitrogenBy similarity1
    Binding sitei335SubstrateBy similarity1
    Binding sitei500Substrate; shared with dimeric partnerBy similarity1
    Binding sitei506Substrate; shared with dimeric partnerBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi55 – 60NADPBy similarity6
    Nucleotide bindingi78 – 80NADPBy similarity3
    Nucleotide bindingi122 – 124NADPBy similarity3

    GO - Molecular functioni

    • phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB

    GO - Biological processi

    • D-gluconate metabolic process Source: UniProtKB-KW
    • oxidation-reduction process Source: UniProtKB
    • pentose-phosphate shunt Source: UniProtKB-UniPathway

    Keywordsi

    Molecular functionOxidoreductase
    Biological processGluconate utilization, Pentose shunt
    LigandNADP

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00410.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    6-phosphogluconate dehydrogenase, decarboxylating 2, chloroplastic (EC:1.1.1.44)
    Gene namesi
    Name:pgdP
    OrganismiSpinacia oleracea (Spinach)
    Taxonomic identifieri3562 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesChenopodiaceaeChenopodioideaeAnserineaeSpinacia

    Subcellular locationi

    GO - Cellular componenti

    • chloroplast Source: UniProtKB

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 44ChloroplastSequence analysisAdd BLAST44
    ChainiPRO_000042110445 – 5376-phosphogluconate dehydrogenase, decarboxylating 2, chloroplasticAdd BLAST493

    Proteomic databases

    PRIDEiQ94KU2.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliQ94KU2.
    SMRiQ94KU2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni176 – 178Substrate bindingBy similarity3
    Regioni233 – 234Substrate bindingBy similarity2

    Sequence similaritiesi

    Keywords - Domaini

    Transit peptide

    Family and domain databases

    Gene3Di1.10.1040.10. 1 hit.
    InterProiView protein in InterPro
    IPR008927. 6-PGluconate_DH_C-like.
    IPR013328. 6PGD_dom_2.
    IPR006114. 6PGDH_C.
    IPR006113. 6PGDH_Gnd/GntZ.
    IPR006115. 6PGDH_NADP-bd.
    IPR016040. NAD(P)-bd_dom.
    IPR006183. Pgluconate_DH.
    PfamiView protein in Pfam
    PF00393. 6PGD. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    PRINTSiPR00076. 6PGDHDRGNASE.
    SMARTiView protein in SMART
    SM01350. 6PGD. 1 hit.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR00873. gnd. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q94KU2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRSEVPSSTS PSFLSPPFIH LPLLSLSSPT PLPHSSSSTF SLFSTMAASQ
    60 70 80 90 100
    IGLVGLAVMG QNLALNIAEK GFPISVYNRT ASKVDETLDR AKSEGDLPLS
    110 120 130 140 150
    GHYTPRDFVL SIERPRSIVI LVKAGSPVDQ TIASLASFME PGDTIIDGGN
    160 170 180 190 200
    EWYQNTERRL SDAHSNGLLY LGMGVSGGEE GARFGPSLMP GGDFQAYDNI
    210 220 230 240 250
    QHILKKVAAQ VDDGPCVTYI GEGGSGNFVK MVHNGIEYGD MQLISEAYDV
    260 270 280 290 300
    LKNVGGLSNE ELGQIFDEWN KSELESFLVE ITADIFKVKD DLADGGLVDK
    310 320 330 340 350
    ILDKTGMKGT GKWTVQQAAE LSVAAPTIAA SLDCRYLSGL KEERENAAKI
    360 370 380 390 400
    LEAAGMKEEV NAIRGGVDKK RLIDDVRQAL YASKICSYAQ GMNLLRAKSA
    410 420 430 440 450
    EMGWDLNLGE LARIWKGGCI IRAVFLDSIK QAYQRNPNLA SLVVDPEFAK
    460 470 480 490 500
    EMVQRQAAWR RVVGLAVSAG ISTPGMCASL AYFDTYRRAR LPANLVQAQR
    510 520 530
    DYFGAHTYER VDLPGSYHTE WSKLARKSDP NVAAALH
    Length:537
    Mass (Da):58,293
    Last modified:December 1, 2001 - v1
    Checksum:i8AB4D8F926B1DA71
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF295670 mRNA. Translation: AAK49897.1.

    Similar proteinsi

    Entry informationi

    Entry namei6PGD2_SPIOL
    AccessioniPrimary (citable) accession number: Q94KU2
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 6, 2013
    Last sequence update: December 1, 2001
    Last modified: May 10, 2017
    This is version 73 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families