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Protein

2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase

Gene

kduD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the reversible reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3-deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH (Ref. 4). To a lesser extent, can also reduce 5-keto-D-gluconate and oxidize D-gluconate and 1,2-propanediol (PubMed:24509771). Together with KduI, seems to play a role in the catabolism of hexuronates under osmotic stress conditions, substituting for the regular hexuronate degrading enzymes UxaABC and UxuAB whose expression is repressed in these conditions (PubMed:23437267). In vitro, also exhibits NADH-dependent 20-ketosteroid reductase activity against eukaryotic steroid hormone 11-deoxycorticosterone (11-DOC), which is converted into the product 4-pregnen-20,21-diol-3-one. In addition to 11-DOC, five other C21 steroid compounds (11-deoxycortisol, cortisol, corticosterone, cortisone, and 21-hydroxypregnenolone) are reduced by KduD, but steroids lacking the hydroxyl group at C21 position, such as pregnenolone, testosterone propionate, cortisone acetate, or progesterone, cannot be used as substrate (PubMed:24509771).3 Publications

Caution

Most strains of E.coli do not exhibit 20-ketosteroid reductase activity against steroid substrates such as 11-DOC, despite containing a full-length kduD gene. This activity is observed in the K12 / DH5-alpha strain, whose disruption of the kdgR gene leads to the constitutive expression of KduD in this strain.1 Publication

Catalytic activityi

2-dehydro-3-deoxy-D-gluconate + NAD+ = (4S)-4,6-dihydroxy-2,5-dioxohexanoate + NADH.1 Publication
4-pregnen-20,21-diol-3-one + NAD+ = 11-deoxycorticosterone + NADH.1 Publication

Kineticsi

kcat is 3.1 min(-1) for 11-DOC reduction. kcat is 16.6 min(-1) for 11-deoxycortisol (RSS) reduction. kcat is 58.3 min(-1) for D-gluconate oxidation. kcat is 30.7 min(-1) for 5-keto-D-gluconate reduction. kcat is 18.3 min(-1) for 1,2-propanediol oxidation.1 Publication
  1. KM=30 mM for 2-keto-3-deoxygluconate1 Publication
  2. KM=0.230 mM for 11-deoxycorticosterone1 Publication
  3. KM=0.190 mM for 11-deoxycortisol1 Publication
  4. KM=544.8 mM for D-gluconate1 Publication
  5. KM=184.5 mM for 5-keto-D-gluconate1 Publication
  6. KM=3231 mM for 1,2-propanediol1 Publication
  7. KM=0.037 mM for NADH1 Publication
  8. KM=0.285 mM for NAD+1 Publication

    pH dependencei

    Optimum pH is 7.0 for the reduction of 11-DOC, and 9.5 for the oxidation of D-gluconate.1 Publication

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius for the reduction of 11-DOC.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei145SubstrateBy similarity1
    Active sitei158Proton acceptorPROSITE-ProRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi14 – 38NADBy similarityAdd BLAST25

    GO - Molecular functioni

    GO - Biological processi

    • D-galacturonate catabolic process Source: EcoCyc
    • D-glucuronate catabolic process Source: EcoCyc

    Keywordsi

    Molecular functionOxidoreductase
    LigandNAD

    Enzyme and pathway databases

    BioCyciEcoCyc:KDUD-MONOMER
    MetaCyc:KDUD-MONOMER

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase1 Publication (EC:1.1.1.1271 Publication)
    Alternative name(s):
    2-deoxy-D-gluconate 3-dehydrogenase1 Publication
    2-keto-3-deoxygluconate 5-dehydrogenase
    2-keto-3-deoxygluconate oxidoreductase1 Publication
    Short name:
    KDG oxidoreductase
    20-ketosteroid reductase1 Publication (EC:1.1.1.-1 Publication)
    Gene namesi
    Name:kduD1 Publication
    Synonyms:ygeC, yqeD
    Ordered Locus Names:b2842, JW2810
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12361 kduD

    Pathology & Biotechi

    Biotechnological usei

    Could be used for the production of valuable bioactive 20-hydroxysteroids; these compounds have potential for pharmaceutical applications as inhibitors of steroid hormone metabolizing enzymes, for the treatment of breast cancer, endometriosis, and prostate diseases in humans.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000547151 – 2532-dehydro-3-deoxy-D-gluconate 5-dehydrogenaseAdd BLAST253

    Proteomic databases

    PaxDbiP37769
    PRIDEiP37769

    Expressioni

    Inductioni

    Is under the control of KdgR repressor (Probable). Its expression is up-regulated in the presence of galacturonate and glucuronate (PubMed:23437267). Is also up-regulated in intestinal E.coli of mice fed a lactose-rich diet and down-regulated in E.coli of mice on a casein-rich diet (PubMed:22427493).1 Publication2 Publications

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    BioGridi4262312, 35 interactors
    IntActiP37769, 2 interactors
    STRINGi316385.ECDH10B_3014

    Structurei

    3D structure databases

    ProteinModelPortaliP37769
    SMRiP37769
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CHR Bacteria
    ENOG410XNW1 LUCA
    InParanoidiP37769
    KOiK00065
    OMAiFELLGAY
    PhylomeDBiP37769

    Family and domain databases

    InterProiView protein in InterPro
    IPR011286 2-deoxy-D-gluc_3_DH
    IPR036291 NAD(P)-bd_dom_sf
    IPR020904 Sc_DH/Rdtase_CS
    IPR002347 SDR_fam
    PRINTSiPR00081 GDHRDH
    PR00080 SDRFAMILY
    SUPFAMiSSF51735 SSF51735, 1 hit
    TIGRFAMsiTIGR01832 kduD, 1 hit
    PROSITEiView protein in PROSITE
    PS00061 ADH_SHORT, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P37769-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MILSAFSLEG KVAVVTGCDT GLGQGMALGL AQAGCDIVGI NIVEPTETIE
    60 70 80 90 100
    QVTALGRRFL SLTADLRKID GIPALLDRAV AEFGHIDILV NNAGLIRRED
    110 120 130 140 150
    ALEFSEKDWD DVMNLNIKSV FFMSQAAAKH FIAQGNGGKI INIASMLSFQ
    160 170 180 190 200
    GGIRVPSYTA SKSGVMGVTR LMANEWAKHN INVNAIAPGY MATNNTQQLR
    210 220 230 240 250
    ADEQRSAEIL DRIPAGRWGL PSDLMGPIVF LASSASDYVN GYTIAVDGGW

    LAR
    Length:253
    Mass (Da):27,070
    Last modified:October 1, 1996 - v2
    Checksum:iC751D4C2CEC6FAA0
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U29581 Genomic DNA Translation: AAB40489.1
    U00096 Genomic DNA Translation: AAC75881.1
    AP009048 Genomic DNA Translation: BAE76911.1
    J03732 Genomic DNA No translation available.
    PIRiC65067
    RefSeqiNP_417319.1, NC_000913.3
    WP_000603502.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC75881; AAC75881; b2842
    BAE76911; BAE76911; BAE76911
    GeneIDi947323
    KEGGiecj:JW2810
    eco:b2842
    PATRICifig|1411691.4.peg.3892

    Similar proteinsi

    Entry informationi

    Entry nameiKDUD_ECOLI
    AccessioniPrimary (citable) accession number: P37769
    Secondary accession number(s): Q2M9Z5
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1996
    Last modified: March 28, 2018
    This is version 134 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health