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Entry version 149 (07 Oct 2020)
Sequence version 2 (01 Nov 1997)
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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

<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

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.

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

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
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei81NADP; via carbonyl oxygenBy similarity1
    Binding sitei134SubstrateBy similarity1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei147Proton acceptorPROSITE-ProRule annotation1
    Binding sitei147NADPBy similarity1
    Binding sitei151NADPBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 bindingi7 – 12NADPBy similarity6
    Nucleotide bindingi32 – 33NADPBy similarity2
    Nucleotide bindingi54 – 55NADPBy similarity2
    Nucleotide bindingi177 – 185NADPBy similarity9

    <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
    LigandNADP

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:EG12345-MONOMER
    MetaCyc:EG12345-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%5Fand%5Ftaxonomy%5Fsection">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:
    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)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:ydfGImported
    Ordered Locus Names:b1539, JW1532
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    GO - Cellular componenti

    <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 in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>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

    <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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000548251 – 248NADP-dependent 3-hydroxy acid dehydrogenase YdfGAdd BLAST248

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...
    jPOSTi
    P39831

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

    More...
    PaxDbi
    P39831

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P39831

    <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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homotetramer.

    1 Publication

    GO - Molecular functioni

    Protein-protein interaction databases

    The Biological General Repository for Interaction Datasets (BioGRID)

    More...
    BioGRIDi
    4261740, 23 interactors
    850445, 1 interactor

    Database of interacting proteins

    More...
    DIPi
    DIP-11696N

    Protein interaction database and analysis system

    More...
    IntActi
    P39831, 13 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    511145.b1539

    <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
    P39831

    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
    COG4221, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_010194_2_10_6

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P39831

    KEGG Orthology (KO)

    More...
    KOi
    K16066

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P39831

    Family and domain databases

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR036291, NAD(P)-bd_dom_sf
    IPR020904, Sc_DH/Rdtase_CS
    IPR002347, SDR_fam

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00106, adh_short, 1 hit

    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

    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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

    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
    <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:i6FECC5FBAA86EA42
    GO

    <p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

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

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti182G → T in X57947 (PubMed:8226676).Curated1

    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
    U00096 Genomic DNA Translation: AAC74612.1
    AP009048 Genomic DNA Translation: BAA15241.1
    X57947 Genomic DNA No translation available.

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    F64908

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_416057.1, NC_000913.3
    WP_000636571.1, NZ_STEB01000003.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC74612; AAC74612; b1539
    BAA15241; BAA15241; BAA15241

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    946085

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW1532
    eco:b1539

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|1411691.4.peg.726

    <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
    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_STEB01000003.1

    3D structure databases

    SMRiP39831
    ModBaseiSearch...

    Protein-protein interaction databases

    BioGRIDi4261740, 23 interactors
    850445, 1 interactor
    DIPiDIP-11696N
    IntActiP39831, 13 interactors
    STRINGi511145.b1539

    Proteomic databases

    jPOSTiP39831
    PaxDbiP39831
    PRIDEiP39831

    Genome annotation databases

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

    Organism-specific databases

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

    More...
    EchoBASEi
    EB2249

    Phylogenomic databases

    eggNOGiCOG4221, Bacteria
    HOGENOMiCLU_010194_2_10_6
    InParanoidiP39831
    KOiK16066
    PhylomeDBiP39831

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12345-MONOMER
    MetaCyc:EG12345-MONOMER

    Miscellaneous databases

    Protein Ontology

    More...
    PROi
    PR:P39831

    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

    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 nameiYDFG_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: P39831
    Secondary accession number(s): P77149, P78161, P78162
    <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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 1, 1997
    Last modified: October 7, 2020
    This is version 149 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

    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
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