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Protein

NADP-dependent 3-hydroxy acid dehydrogenase

Gene

YMR226C

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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.1 Publication

Catalytic activityi

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

Kineticsi

The highest catalytic efficiency was observed with L-allo-threonine.1 Publication

  1. KM=0.5 mM for NADP+ (at pH 9 and at 30 degrees Celsius)1 Publication
  2. KM=95 mM for L-serine (at pH 9 and at 30 degrees Celsius)1 Publication
  3. KM=71 mM for D-serine (at pH 9 and at 30 degrees Celsius)1 Publication
  4. KM=7 mM for D-threonine (at pH 9 and at 30 degrees Celsius)1 Publication
  5. KM=3 mM for L-allo-threonine (at pH 9 and at 30 degrees Celsius)1 Publication
  6. KM=36 mM for L-3-hydroxyisobutyrate (at pH 9 and at 30 degrees Celsius)1 Publication
  7. KM=57 mM for D-3-hydroxyisobutyrate (at pH 9 and at 30 degrees Celsius)1 Publication
  8. KM=95 mM for L-3-hydroxybutyrate (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 7.5 to 10.5.1 Publication

    Temperature dependencei

    Stable up to 40 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei102 – 1021NADP; via carbonyl oxygen1 Publication
    Binding sitei155 – 1551SubstrateBy similarity
    Active sitei168 – 1681Proton acceptorPROSITE-ProRule annotation
    Binding sitei168 – 1681NADP1 Publication
    Binding sitei172 – 1721NADP1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi20 – 256NADP1 Publication
    Nucleotide bindingi48 – 492NADP1 Publication
    Nucleotide bindingi75 – 762NADP1 Publication
    Nucleotide bindingi198 – 2058NADP1 Publication

    GO - Molecular functioni

    • carbonyl reductase (NADPH) activity Source: SGD
    • oxidoreductase activity Source: SGD
    • serine 3-dehydrogenase activity Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciYEAST:G3O-32907-MONOMER.
    ReactomeiR-SCE-2142700. Synthesis of Lipoxins (LX).

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NADP-dependent 3-hydroxy acid dehydrogenase1 Publication
    Alternative name(s):
    L-allo-threonine dehydrogenase1 Publication (EC:1.1.1.3811 Publication)
    Gene namesi
    Ordered Locus Names:YMR226CImported
    ORF Names:YM9959.08C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XIII

    Organism-specific databases

    EuPathDBiFungiDB:YMR226C.
    SGDiS000004839. YMR226C.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 267267NADP-dependent 3-hydroxy acid dehydrogenasePRO_0000054873Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei260 – 2601PhosphoserineCombined sources

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ05016.
    PeptideAtlasiQ05016.
    PRIDEiQ05016.
    TopDownProteomicsiQ05016.

    PTM databases

    iPTMnetiQ05016.

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    BioGridi35404. 38 interactions.
    DIPiDIP-1671N.
    IntActiQ05016. 4 interactions.
    MINTiMINT-409559.

    Structurei

    Secondary structure

    1
    267
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 117Combined sources
    Beta strandi15 – 206Combined sources
    Helixi24 – 3613Combined sources
    Turni37 – 393Combined sources
    Beta strandi41 – 488Combined sources
    Helixi50 – 6314Combined sources
    Beta strandi68 – 736Combined sources
    Helixi79 – 813Combined sources
    Helixi82 – 876Combined sources
    Helixi91 – 933Combined sources
    Beta strandi98 – 1014Combined sources
    Helixi117 – 12711Combined sources
    Helixi129 – 14517Combined sources
    Beta strandi149 – 1535Combined sources
    Helixi156 – 1583Combined sources
    Helixi166 – 18520Combined sources
    Turni186 – 1883Combined sources
    Beta strandi192 – 1998Combined sources
    Beta strandi201 – 2044Combined sources
    Helixi205 – 2095Combined sources
    Turni210 – 2123Combined sources
    Helixi214 – 2218Combined sources
    Helixi229 – 24012Combined sources
    Beta strandi246 – 25510Combined sources
    Beta strandi258 – 2603Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3RKUX-ray2.60A/B/C/D1-267[»]
    ProteinModelPortaliQ05016.
    SMRiQ05016. Positions 1-267.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    GeneTreeiENSGT00840000129887.
    InParanoidiQ05016.
    KOiK16066.
    OMAiMEMGSAI.
    OrthoDBiEOG70612F.

    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.

    Q05016-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSQGRKAAER LAKKTVLITG ASAGIGKATA LEYLEASNGD MKLILAARRL
    60 70 80 90 100
    EKLEELKKTI DQEFPNAKVH VAQLDITQAE KIKPFIENLP QEFKDIDILV
    110 120 130 140 150
    NNAGKALGSD RVGQIATEDI QDVFDTNVTA LINITQAVLP IFQAKNSGDI
    160 170 180 190 200
    VNLGSIAGRD AYPTGSIYCA SKFAVGAFTD SLRKELINTK IRVILIAPGL
    210 220 230 240 250
    VETEFSLVRY RGNEEQAKNV YKDTTPLMAD DVADLIVYAT SRKQNTVIAD
    260
    TLIFPTNQAS PHHIFRG
    Length:267
    Mass (Da):29,158
    Last modified:November 1, 1997 - v1
    Checksum:i77FCD713F724A9D7
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z49939 Genomic DNA. Translation: CAA90197.1.
    BK006946 Genomic DNA. Translation: DAA10125.1.
    PIRiS57593.
    RefSeqiNP_013953.1. NM_001182733.1.

    Genome annotation databases

    EnsemblFungiiYMR226C; YMR226C; YMR226C.
    GeneIDi855266.
    KEGGisce:YMR226C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z49939 Genomic DNA. Translation: CAA90197.1.
    BK006946 Genomic DNA. Translation: DAA10125.1.
    PIRiS57593.
    RefSeqiNP_013953.1. NM_001182733.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3RKUX-ray2.60A/B/C/D1-267[»]
    ProteinModelPortaliQ05016.
    SMRiQ05016. Positions 1-267.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi35404. 38 interactions.
    DIPiDIP-1671N.
    IntActiQ05016. 4 interactions.
    MINTiMINT-409559.

    PTM databases

    iPTMnetiQ05016.

    Proteomic databases

    MaxQBiQ05016.
    PeptideAtlasiQ05016.
    PRIDEiQ05016.
    TopDownProteomicsiQ05016.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYMR226C; YMR226C; YMR226C.
    GeneIDi855266.
    KEGGisce:YMR226C.

    Organism-specific databases

    EuPathDBiFungiDB:YMR226C.
    SGDiS000004839. YMR226C.

    Phylogenomic databases

    GeneTreeiENSGT00840000129887.
    InParanoidiQ05016.
    KOiK16066.
    OMAiMEMGSAI.
    OrthoDBiEOG70612F.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-32907-MONOMER.
    ReactomeiR-SCE-2142700. Synthesis of Lipoxins (LX).

    Miscellaneous databases

    PROiQ05016.

    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Characterization of short-chain dehydrogenase/reductase homologues of Escherichia coli (YdfG) and Saccharomyces cerevisiae (YMR226C)."
      Fujisawa H., Nagata S., Misono H.
      Biochim. Biophys. Acta 1645:89-94(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-14, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, SUBUNIT.
    4. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    6. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. "Substrate fingerprint and the structure of NADP(+)-dependent serine dehydrogenase from Saccharomyces cerevisiae complexed with NADP(+)."
      Huether R., Pacheco C.M., Duax W.L.
      Submitted (APR-2011) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH NADP.

    Entry informationi

    Entry nameiYM71_YEAST
    AccessioniPrimary (citable) accession number: Q05016
    Secondary accession number(s): D6W051
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: June 8, 2016
    This is version 130 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 3210 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

    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.