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Entry version 140 (18 Sep 2019)
Sequence version 2 (01 Oct 1996)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei145SubstrateBy similarity1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei158Proton acceptorPROSITE-ProRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi14 – 38NADBy similarityAdd BLAST25

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionOxidoreductase
    LigandNAD

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:KDUD-MONOMER
    ECOL316407:JW2810-MONOMER
    MetaCyc:KDUD-MONOMER

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:kduD1 Publication
    Synonyms:ygeC, yqeD
    Ordered Locus Names:b2842, JW2810
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    Escherichia coli strain K12 genome database

    More...
    EcoGenei
    EG12361 kduD

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    <p>This subsection of the ‘Pathology and Biotech’ section describes the use of a specific protein in the biotechnological industry.<p><a href='/help/biotechnological_use' target='_top'>More...</a></p>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

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000547151 – 2532-dehydro-3-deoxy-D-gluconate 5-dehydrogenaseAdd BLAST253

    Proteomic databases

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    P37769

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P37769

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    <p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>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

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homotetramer.

    1 Publication

    Protein-protein interaction databases

    The Biological General Repository for Interaction Datasets (BioGrid)

    More...
    BioGridi
    4262312, 35 interactors

    Protein interaction database and analysis system

    More...
    IntActi
    P37769, 2 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    511145.b2842

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    P37769

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4105CHR Bacteria
    ENOG410XNW1 LUCA

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P37769

    KEGG Orthology (KO)

    More...
    KOi
    K00065

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P37769

    Family and domain databases

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR011286 2-deoxy-D-gluc_3_DH
    IPR036291 NAD(P)-bd_dom_sf
    IPR020904 Sc_DH/Rdtase_CS
    IPR002347 SDR_fam

    Protein Motif fingerprint database; a protein domain database

    More...
    PRINTSi
    PR00081 GDHRDH
    PR00080 SDRFAMILY

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51735 SSF51735, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01832 kduD, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00061 ADH_SHORT, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC751D4C2CEC6FAA0
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    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.

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    C65067

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_417319.1, NC_000913.3
    WP_000603502.1, NZ_LN832404.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC75881; AAC75881; b2842
    BAE76911; BAE76911; BAE76911

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    947323

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW2810
    eco:b2842

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|1411691.4.peg.3892

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

    SMRiP37769
    ModBaseiSearch...

    Protein-protein interaction databases

    BioGridi4262312, 35 interactors
    IntActiP37769, 2 interactors
    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
    PATRICifig|1411691.4.peg.3892

    Organism-specific databases

    EchoBASE - an integrated post-genomic database for E. coli

    More...
    EchoBASEi
    EB2264
    EcoGeneiEG12361 kduD

    Phylogenomic databases

    eggNOGiENOG4105CHR Bacteria
    ENOG410XNW1 LUCA
    InParanoidiP37769
    KOiK00065
    PhylomeDBiP37769

    Enzyme and pathway databases

    BioCyciEcoCyc:KDUD-MONOMER
    ECOL316407:JW2810-MONOMER
    MetaCyc:KDUD-MONOMER

    Miscellaneous databases

    Protein Ontology

    More...
    PROi
    PR:P37769

    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

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiKDUD_ECOLI
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P37769
    Secondary accession number(s): Q2M9Z5
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1996
    Last modified: September 18, 2019
    This is version 140 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
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