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Protein

D-galactonate dehydratase

Gene

dgoD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-D-galactonate.2 Publications

Miscellaneous

Reaction proceeds via an anti dehydration.

Catalytic activityi

D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O.

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

Kineticsi

  1. KM=1.5 mM for D-galactonate1 Publication

    Pathwayi: D-galactonate degradation

    This protein is involved in step 1 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate.1 Publication
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. D-galactonate dehydratase (dgoD)
    2. 2-dehydro-3-deoxygalactonokinase (dgoK)
    3. 2-dehydro-3-deoxy-6-phosphogalactonate aldolase (dgoA)
    This subpathway is part of the pathway D-galactonate degradation, which is itself part of Carbohydrate acid metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate, the pathway D-galactonate degradation and in Carbohydrate acid metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi183MagnesiumBy similarity1
    Active sitei185Proton donor1
    Metal bindingi209MagnesiumBy similarity1
    Metal bindingi235MagnesiumBy similarity1
    Sitei258Increases basicity of active site HisBy similarity1
    Active sitei285Proton acceptor1
    Sitei310Transition state stabilizer1

    GO - Molecular functioni

    GO - Biological processi

    • cellular amino acid catabolic process Source: InterPro
    • D-galactonate catabolic process Source: EcoCyc

    Keywordsi

    Molecular functionLyase
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:GALACTONATE-DEHYDRATASE-MONOMER.
    MetaCyc:GALACTONATE-DEHYDRATASE-MONOMER.
    UniPathwayiUPA00081; UER00518.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-galactonate dehydratase (EC:4.2.1.6)
    Short name:
    GalD
    Gene namesi
    Name:dgoD
    Synonyms:yidU
    Ordered Locus Names:b4478, JW5629
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG20050. dgoD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi185H → N or Q: Loss of activity. 1 Publication1
    Mutagenesisi285H → N: Loss of activity. 1 Publication1
    Mutagenesisi310E → Q: Loss of activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001712591 – 382D-galactonate dehydrataseAdd BLAST382

    Proteomic databases

    PaxDbiQ6BF17.
    PRIDEiQ6BF17.

    Expressioni

    Inductioni

    Induced by galactonate, but not by glycerol, gluconate or galactose. Repressed by glucose.2 Publications

    Interactioni

    Protein-protein interaction databases

    STRINGi511145.b4478.

    Structurei

    3D structure databases

    ProteinModelPortaliQ6BF17.
    SMRiQ6BF17.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CXK. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113756.
    InParanoidiQ6BF17.
    KOiK01684.
    OMAiLHRPMAK.
    PhylomeDBiQ6BF17.

    Family and domain databases

    CDDicd03325. D-galactonate_dehydratase. 1 hit.
    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    HAMAPiMF_01289. Galacton_dehydrat. 1 hit.
    InterProiView protein in InterPro
    IPR034390. Enolase-like_superfamily.
    IPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR023592. Galactonate_deHydtase.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    PfamiView protein in Pfam
    PF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    SFLDiSFLDF00003. D-galactonate_dehydratase. 1 hit.
    SFLDS00001. Enolase. 1 hit.
    SMARTiView protein in SMART
    SM00922. MR_MLE. 1 hit.
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    PROSITEiView protein in PROSITE
    PS00908. MR_MLE_1. 1 hit.
    PS00909. MR_MLE_2. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q6BF17-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKITKITTYR LPPRWMFLKI ETDEGVVGWG EPVIEGRART VEAAVHELGD
    60 70 80 90 100
    YLIGQDPSRI NDLWQVMYRA GFYRGGPILM SAIAGIDQAL WDIKGKVLNA
    110 120 130 140 150
    PVWQLMGGLV RDKIKAYSWV GGDRPADVID GIKTLREIGF DTFKLNGCEE
    160 170 180 190 200
    LGLIDNSRAV DAAVNTVAQI REAFGNQIEF GLDFHGRVSA PMAKVLIKEL
    210 220 230 240 250
    EPYRPLFIEE PVLAEQAEYY PKLAAQTHIP LAAGERMFSR FDFKRVLEAG
    260 270 280 290 300
    GISILQPDLS HAGGITECYK IAGMAEAYDV TLAPHCPLGP IALAACLHID
    310 320 330 340 350
    FVSYNAVLQE QSMGIHYNKG AELLDFVKNK EDFSMVGGFF KPLTKPGLGV
    360 370 380
    EIDEAKVIEF SKNAPDWRNP LWRHEDNSVA EW
    Length:382
    Mass (Da):42,523
    Last modified:August 16, 2004 - v1
    Checksum:iB38D4E0B95FD7041
    GO

    Sequence cautioni

    The sequence AAA62044 differs from that shown. Reason: Frameshift at position 1. The frameshift in position 1 caused the prediction of an ORF that fused dgoA and dgoD.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti137E → Q in AAA62044 (PubMed:7686882).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10328 Genomic DNA. Translation: AAA62044.1. Frameshift.
    U00096 Genomic DNA. Translation: AAT48197.1.
    AP009048 Genomic DNA. Translation: BAE77602.1.
    PIRiE65171.
    RefSeqiWP_000705001.1. NZ_LN832404.1.
    YP_026237.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAT48197; AAT48197; b4478.
    BAE77602; BAE77602; BAE77602.
    GeneIDi2847765.
    KEGGiecj:JW5629.
    eco:b4478.
    PATRICi32122879. VBIEscCol129921_3815.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10328 Genomic DNA. Translation: AAA62044.1. Frameshift.
    U00096 Genomic DNA. Translation: AAT48197.1.
    AP009048 Genomic DNA. Translation: BAE77602.1.
    PIRiE65171.
    RefSeqiWP_000705001.1. NZ_LN832404.1.
    YP_026237.1. NC_000913.3.

    3D structure databases

    ProteinModelPortaliQ6BF17.
    SMRiQ6BF17.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi511145.b4478.

    Proteomic databases

    PaxDbiQ6BF17.
    PRIDEiQ6BF17.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAT48197; AAT48197; b4478.
    BAE77602; BAE77602; BAE77602.
    GeneIDi2847765.
    KEGGiecj:JW5629.
    eco:b4478.
    PATRICi32122879. VBIEscCol129921_3815.

    Organism-specific databases

    EchoBASEiEB4309.
    EcoGeneiEG20050. dgoD.

    Phylogenomic databases

    eggNOGiENOG4105CXK. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113756.
    InParanoidiQ6BF17.
    KOiK01684.
    OMAiLHRPMAK.
    PhylomeDBiQ6BF17.

    Enzyme and pathway databases

    UniPathwayiUPA00081; UER00518.
    BioCyciEcoCyc:GALACTONATE-DEHYDRATASE-MONOMER.
    MetaCyc:GALACTONATE-DEHYDRATASE-MONOMER.

    Miscellaneous databases

    PROiPR:Q6BF17.

    Family and domain databases

    CDDicd03325. D-galactonate_dehydratase. 1 hit.
    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    HAMAPiMF_01289. Galacton_dehydrat. 1 hit.
    InterProiView protein in InterPro
    IPR034390. Enolase-like_superfamily.
    IPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR023592. Galactonate_deHydtase.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    PfamiView protein in Pfam
    PF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    SFLDiSFLDF00003. D-galactonate_dehydratase. 1 hit.
    SFLDS00001. Enolase. 1 hit.
    SMARTiView protein in SMART
    SM00922. MR_MLE. 1 hit.
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    PROSITEiView protein in PROSITE
    PS00908. MR_MLE_1. 1 hit.
    PS00909. MR_MLE_2. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDGOD_ECOLI
    AccessioniPrimary (citable) accession number: Q6BF17
    Secondary accession number(s): P31458, Q2M804
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 23, 2004
    Last sequence update: August 16, 2004
    Last modified: April 12, 2017
    This is version 103 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    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. 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.