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Protein

NADP-dependent 3-hydroxy acid dehydrogenase YdfG

Gene

ydfG

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

Functioni

NADP-dependent dehydrogenase with broad substrate specificity acting on 3-hydroxy acids. Catalyzes the NADP-dependent oxidation of L-allo-threonine to L-2-amino-3-keto-butyrate, which is spontaneously decarboxylated into aminoacetone. Also acts on D-threonine, L-serine, D-serine, D-3-hydroxyisobutyrate, L-3-hydroxyisobutyrate, D-glycerate and L-glycerate (PubMed:12535615). Able to catalyze the reduction of the malonic semialdehyde to 3-hydroxypropionic acid. YdfG is apparently supplementing RutE, the presumed malonic semialdehyde reductase involved in pyrimidine degradation since both are able to detoxify malonic semialdehyde (PubMed:20400551).2 Publications

Miscellaneous

L-threonine, D-allo-threonine, DL-threo-3-phenyl-serine, malonate, DL-malate, citrate, isocitrate, DL-lactate, DL-tartrate, gluconate, glycerol and glycolate are inert as substrates.

Catalytic activityi

3-hydroxypropanoate + NADP+ = 3-oxopropanoate + NADPH.1 Publication
L-allo-threonine + NADP+ = aminoacetone + CO2 + NADPH.1 Publication

Kineticsi

The highest catalytic efficiency was observed with L-allo-threonine.1 Publication
  1. KM=0.54 mM for NADP+ (at pH 9 and at 30 degrees Celsius)1 Publication
  2. KM=40 mM for L-serine (at pH 9 and at 30 degrees Celsius)1 Publication
  3. KM=69 mM for D-serine (at pH 9 and at 30 degrees Celsius)1 Publication
  4. KM=60 mM for D-threonine (at pH 9 and at 30 degrees Celsius)1 Publication
  5. KM=29 mM for L-allo-threonine (at pH 9 and at 30 degrees Celsius)1 Publication
  6. KM=33 mM for L-glycerate (at pH 9 and at 30 degrees Celsius)1 Publication
  7. KM=50 mM for D-glycerate (at pH 9 and at 30 degrees Celsius)1 Publication
  8. KM=60 mM for L-3-hydroxyisobutyrate (at pH 9 and at 30 degrees Celsius)1 Publication
  9. KM=61 mM for D-3-hydroxyisobutyrate (at pH 9 and at 30 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is about 8.5 for the oxidation of L-serine. Stable from pH 6.5 to 10.0.1 Publication

    Temperature dependencei

    Still active after heating at 55 degrees Celsius for 80 minutes.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei81NADP; via carbonyl oxygenBy similarity1
    Binding sitei134SubstrateBy similarity1
    Active sitei147Proton acceptorPROSITE-ProRule annotation1
    Binding sitei147NADPBy similarity1
    Binding sitei151NADPBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi7 – 12NADPBy similarity6
    Nucleotide bindingi32 – 33NADPBy similarity2
    Nucleotide bindingi54 – 55NADPBy similarity2
    Nucleotide bindingi177 – 185NADPBy similarity9

    GO - Molecular functioni

    • 3-hydroxypropionate dehydrogenase (NADP+) activity Source: EcoCyc
    • serine 3-dehydrogenase activity Source: EcoCyc

    GO - Biological processi

    • uracil catabolic process Source: UniProtKB

    Keywordsi

    Molecular functionOxidoreductase
    LigandNADP

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12345-MONOMER
    MetaCyc:EG12345-MONOMER

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NADP-dependent 3-hydroxy acid dehydrogenase YdfG1 Publication
    Alternative name(s):
    L-allo-threonine dehydrogenase1 Publication (EC:1.1.1.3811 Publication)
    Malonic semialdehyde reductase1 Publication (EC:1.1.1.2981 Publication)
    Gene namesi
    Name:ydfGImported
    Ordered Locus Names:b1539, JW1532
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12345 ydfG

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene grow poorly on pyrimidine nucleosides and bases as the sole source of nitrogen at room temperature indicating a probably accumulation of a toxic intermediate, the malonic semialdehyde.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000548251 – 248NADP-dependent 3-hydroxy acid dehydrogenase YdfGAdd BLAST248

    Proteomic databases

    EPDiP39831
    PaxDbiP39831
    PRIDEiP39831

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    BioGridi4261740, 23 interactors
    DIPiDIP-11696N
    IntActiP39831, 13 interactors
    STRINGi316385.ECDH10B_1670

    Structurei

    3D structure databases

    ProteinModelPortaliP39831
    SMRiP39831
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105EMU Bacteria
    COG4221 LUCA
    InParanoidiP39831
    KOiK16066
    OMAiWRWMWET
    PhylomeDBiP39831

    Family and domain databases

    InterProiView protein in InterPro
    IPR036291 NAD(P)-bd_dom_sf
    IPR020904 Sc_DH/Rdtase_CS
    IPR002347 SDR_fam
    PfamiView protein in Pfam
    PF00106 adh_short, 1 hit
    PRINTSiPR00081 GDHRDH
    PR00080 SDRFAMILY
    SUPFAMiSSF51735 SSF51735, 1 hit
    PROSITEiView protein in PROSITE
    PS00061 ADH_SHORT, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P39831-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIVLVTGATA GFGECITRRF IQQGHKVIAT GRRQERLQEL KDELGDNLYI
    60 70 80 90 100
    AQLDVRNRAA IEEMLASLPA EWCNIDILVN NAGLALGMEP AHKASVEDWE
    110 120 130 140 150
    TMIDTNNKGL VYMTRAVLPG MVERNHGHII NIGSTAGSWP YAGGNVYGAT
    160 170 180 190 200
    KAFVRQFSLN LRTDLHGTAV RVTDIEPGLV GGTEFSNVRF KGDDGKAEKT
    210 220 230 240
    YQNTVALTPE DVSEAVWWVS TLPAHVNINT LEMMPVTQSY AGLNVHRQ
    Length:248
    Mass (Da):27,249
    Last modified:November 1, 1997 - v2
    Checksum:i6FECC5FBAA86EA42
    GO

    Sequence cautioni

    The sequence X57947 differs from that shown. Reason: Frameshift at position 58.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti182G → T in X57947 (PubMed:8226676).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA Translation: AAC74612.1
    AP009048 Genomic DNA Translation: BAA15241.1
    X57947 Genomic DNA No translation available.
    PIRiF64908
    RefSeqiNP_416057.1, NC_000913.3
    WP_000636571.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC74612; AAC74612; b1539
    BAA15241; BAA15241; BAA15241
    GeneIDi946085
    KEGGiecj:JW1532
    eco:b1539
    PATRICifig|1411691.4.peg.726

    Similar proteinsi

    Entry informationi

    Entry nameiYDFG_ECOLI
    AccessioniPrimary (citable) accession number: P39831
    Secondary accession number(s): P77149, P78161, P78162
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 1, 1997
    Last modified: March 28, 2018
    This is version 133 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, Direct protein sequencing, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health