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Protein

NADP-dependent 3-hydroxy acid dehydrogenase YdfG

Gene

ydfG

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

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

Manual assertion based on experiment ini

  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
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12345-MONOMER.
    ECOL316407:JW1532-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
    Complete GO annotation...

    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. 16 interactors.
    DIPiDIP-11696N.
    IntActiP39831. 9 interactors.
    STRINGi511145.b1539.

    Structurei

    3D structure databases

    ProteinModelPortaliP39831.
    SMRiP39831.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105EMU. Bacteria.
    COG4221. LUCA.
    InParanoidiP39831.
    KOiK16066.
    OMAiSTAGNWP.
    PhylomeDBiP39831.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR016040. NAD(P)-bd_dom.
    IPR020904. Sc_DH/Rdtase_CS.
    IPR002347. SDR_fam.
    [Graphical view]
    PANTHERiPTHR24322. PTHR24322. 2 hits.
    PfamiPF00106. adh_short. 1 hit.
    [Graphical view]
    PRINTSiPR00081. GDHRDH.
    PR00080. SDRFAMILY.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00061. ADH_SHORT. 1 hit.
    [Graphical view]

    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.
    PATRICi32118378. VBIEscCol129921_1609.

    Cross-referencesi

    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.

    3D structure databases

    ProteinModelPortaliP39831.
    SMRiP39831.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261740. 16 interactors.
    DIPiDIP-11696N.
    IntActiP39831. 9 interactors.
    STRINGi511145.b1539.

    Proteomic databases

    EPDiP39831.
    PaxDbiP39831.
    PRIDEiP39831.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74612; AAC74612; b1539.
    BAA15241; BAA15241; BAA15241.
    GeneIDi946085.
    KEGGiecj:JW1532.
    eco:b1539.
    PATRICi32118378. VBIEscCol129921_1609.

    Organism-specific databases

    EchoBASEiEB2249.
    EcoGeneiEG12345. ydfG.

    Phylogenomic databases

    eggNOGiENOG4105EMU. Bacteria.
    COG4221. LUCA.
    InParanoidiP39831.
    KOiK16066.
    OMAiSTAGNWP.
    PhylomeDBiP39831.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12345-MONOMER.
    ECOL316407:JW1532-MONOMER.
    MetaCyc:EG12345-MONOMER.

    Miscellaneous databases

    PROiP39831.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR016040. NAD(P)-bd_dom.
    IPR020904. Sc_DH/Rdtase_CS.
    IPR002347. SDR_fam.
    [Graphical view]
    PANTHERiPTHR24322. PTHR24322. 2 hits.
    PfamiPF00106. adh_short. 1 hit.
    [Graphical view]
    PRINTSiPR00081. GDHRDH.
    PR00080. SDRFAMILY.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00061. ADH_SHORT. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYDFG_ECOLI
    AccessioniPrimary (citable) accession number: P39831
    Secondary accession number(s): P77149, P78161, P78162
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 1, 1997
    Last modified: November 2, 2016
    This is version 123 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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.

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, 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.