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Protein

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

Gene

kduD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei145 – 1451SubstrateBy similarity
    Active sitei158 – 1581Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi14 – 3825NADBy similarityAdd
    BLAST

    GO - Molecular functioni

    GO - Biological processi

    • D-galacturonate catabolic process Source: EcoCyc
    • D-glucuronate catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciEcoCyc:KDUD-MONOMER.
    ECOL316407:JW2810-MONOMER.
    RETL1328306-WGS:GSTH-5166-MONOMER.
    RETL1328306-WGS:GSTH-6266-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    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)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2532532-dehydro-3-deoxy-D-gluconate 5-dehydrogenasePRO_0000054715Add
    BLAST

    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. 22 interactions.
    IntActiP37769. 2 interactions.
    STRINGi511145.b2842.

    Structurei

    3D structure databases

    ProteinModelPortaliP37769.
    SMRiP37769. Positions 1-253.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CHR. Bacteria.
    ENOG410XNW1. LUCA.
    InParanoidiP37769.
    KOiK00065.
    OMAiDASAYIH.
    PhylomeDBiP37769.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR011286. 2-deoxy-D-gluc_3_DH.
    IPR016040. NAD(P)-bd_dom.
    IPR020904. Sc_DH/Rdtase_CS.
    IPR002347. SDR_fam.
    [Graphical view]
    PANTHERiPTHR24322. PTHR24322. 2 hits.
    PRINTSiPR00081. GDHRDH.
    PR00080. SDRFAMILY.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01832. kduD. 1 hit.
    PROSITEiPS00061. ADH_SHORT. 1 hit.
    [Graphical view]

    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.
    PATRICi32121102. VBIEscCol129921_2940.

    Cross-referencesi

    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.

    3D structure databases

    ProteinModelPortaliP37769.
    SMRiP37769. Positions 1-253.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262312. 22 interactions.
    IntActiP37769. 2 interactions.
    STRINGi511145.b2842.

    Proteomic databases

    PaxDbiP37769.
    PRIDEiP37769.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75881; AAC75881; b2842.
    BAE76911; BAE76911; BAE76911.
    GeneIDi947323.
    KEGGiecj:JW2810.
    eco:b2842.
    PATRICi32121102. VBIEscCol129921_2940.

    Organism-specific databases

    EchoBASEiEB2264.
    EcoGeneiEG12361. kduD.

    Phylogenomic databases

    eggNOGiENOG4105CHR. Bacteria.
    ENOG410XNW1. LUCA.
    InParanoidiP37769.
    KOiK00065.
    OMAiDASAYIH.
    PhylomeDBiP37769.

    Enzyme and pathway databases

    BioCyciEcoCyc:KDUD-MONOMER.
    ECOL316407:JW2810-MONOMER.
    RETL1328306-WGS:GSTH-5166-MONOMER.
    RETL1328306-WGS:GSTH-6266-MONOMER.

    Miscellaneous databases

    PROiP37769.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR011286. 2-deoxy-D-gluc_3_DH.
    IPR016040. NAD(P)-bd_dom.
    IPR020904. Sc_DH/Rdtase_CS.
    IPR002347. SDR_fam.
    [Graphical view]
    PANTHERiPTHR24322. PTHR24322. 2 hits.
    PRINTSiPR00081. GDHRDH.
    PR00080. SDRFAMILY.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01832. kduD. 1 hit.
    PROSITEiPS00061. ADH_SHORT. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiKDUD_ECOLI
    AccessioniPrimary (citable) accession number: P37769
    Secondary accession number(s): Q2M9Z5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1996
    Last modified: September 7, 2016
    This is version 124 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. 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.