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Protein

D-3-phosphoglycerate dehydrogenase 1

Gene

SER3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.1 Publication

Miscellaneous

Present with 7670 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.
(R)-2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.1 Publication

Kineticsi

kcat is 0.2 sec(-1) for 2-oxoglutarate reduction.1 Publication
  1. KM=49 µM for 2-oxoglutarate1 Publication

    Pathwayi: L-serine biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. D-3-phosphoglycerate dehydrogenase 2 (SER33), D-3-phosphoglycerate dehydrogenase 1 (SER3)
    2. Phosphoserine aminotransferase (SER1)
    3. Phosphoserine phosphatase (SER2)
    This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei228NADBy similarity1
    Active sitei287By similarity1
    Binding sitei311NADBy similarity1
    Active sitei316By similarity1
    Active sitei347Proton donorBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi208 – 209NADBy similarity2
    Nucleotide bindingi285 – 287NADBy similarity3
    Nucleotide bindingi347 – 350NADBy similarity4

    GO - Molecular functioni

    • alpha-ketoglutarate reductase activity Source: SGD
    • NAD binding Source: InterPro
    • phosphoglycerate dehydrogenase activity Source: SGD

    GO - Biological processi

    Keywordsi

    Molecular functionOxidoreductase
    Biological processAmino-acid biosynthesis, Serine biosynthesis
    LigandNAD

    Enzyme and pathway databases

    BioCyciYEAST:YER081W-MONOMER
    ReactomeiR-SCE-977347 Serine biosynthesis
    UniPathwayi
    UPA00135;UER00196

    Protein family/group databases

    MoonDBiP40054 Predicted

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-3-phosphoglycerate dehydrogenase 1 (EC:1.1.1.95)
    Short name:
    3-PGDH 1
    Alternative name(s):
    2-oxoglutarate reductaseCurated (EC:1.1.1.3991 Publication)
    Gene namesi
    Name:SER3
    Ordered Locus Names:YER081W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome V

    Organism-specific databases

    SGDiS000000883 SER3

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000760181 – 469D-3-phosphoglycerate dehydrogenase 1Add BLAST469

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei22PhosphoserineCombined sources1
    Modified residuei29PhosphoserineBy similarity1
    Modified residuei33PhosphoserineBy similarity1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP40054
    PaxDbiP40054
    PRIDEiP40054

    PTM databases

    iPTMnetiP40054

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    SER33P405103EBI-16961,EBI-16821

    Protein-protein interaction databases

    BioGridi36826, 70 interactors
    DIPiDIP-5336N
    IntActiP40054, 7 interactors
    MINTiP40054
    STRINGi4932.YER081W

    Structurei

    3D structure databases

    ProteinModelPortaliP40054
    SMRiP40054
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini399 – 469ACTPROSITE-ProRule annotationAdd BLAST71

    Sequence similaritiesi

    Phylogenomic databases

    GeneTreeiENSGT00530000063021
    HOGENOMiHOG000136696
    InParanoidiP40054
    KOiK00058
    OMAiYHAIGIR
    OrthoDBiEOG092C2PBN

    Family and domain databases

    InterProiView protein in InterPro
    IPR002912 ACT_dom
    IPR006139 D-isomer_2_OHA_DH_cat_dom
    IPR029753 D-isomer_DH_CS
    IPR029752 D-isomer_DH_CS1
    IPR006140 D-isomer_DH_NAD-bd
    IPR036291 NAD(P)-bd_dom_sf
    IPR029015 PGDH_2
    PANTHERiPTHR10996:SF165 PTHR10996:SF165, 1 hit
    PfamiView protein in Pfam
    PF00389 2-Hacid_dh, 1 hit
    PF02826 2-Hacid_dh_C, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit
    PROSITEiView protein in PROSITE
    PS51671 ACT, 1 hit
    PS00065 D_2_HYDROXYACID_DH_1, 1 hit
    PS00670 D_2_HYDROXYACID_DH_2, 1 hit
    PS00671 D_2_HYDROXYACID_DH_3, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P40054-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MTSIDINNLQ NTFQQAMNMS GSPGAVCTSP TQSFMNTVPQ RLNAVKHPKI
    60 70 80 90 100
    LKPFSTGDMK ILLLENVNQT AITIFEEQGY QVEFYKSSLP EEELIEKIKD
    110 120 130 140 150
    VHAIGIRSKT RLTSNVLQHA KNLVCIGCFC IGTNQVDLDY ATSRGIAVFN
    160 170 180 190 200
    SPFSNSRSVA ELVIAEIISL ARQLGDRSIE LHTGTWNKVA ARCWEVRGKT
    210 220 230 240 250
    LGIIGYGHIG SQLSVLAEAM GLHVLYYDIV TIMALGTARQ VSTLDELLNK
    260 270 280 290 300
    SDFVTLHVPA TPETEKMLSA PQFAAMKDGA YVINASRGTV VDIPSLIQAV
    310 320 330 340 350
    KANKIAGAAL DVYPHEPAKN GEGSFNDELN SWTSELVSLP NIILTPHIGG
    360 370 380 390 400
    STEEAQSSIG IEVATALSKY INEGNSVGSV NFPEVALKSL SYDQENTVRV
    410 420 430 440 450
    LYIHQNVPGV LKTVNDILSN HNIEKQFSDS NGEIAYLMAD ISSVDQSDIK
    460
    DIYEQLNQTS AKISIRLLY
    Length:469
    Mass (Da):51,193
    Last modified:February 1, 1995 - v1
    Checksum:iE1E69070BF41A87C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18839 Genomic DNA Translation: AAB64636.1
    BK006939 Genomic DNA Translation: DAA07742.1
    PIRiS50584
    RefSeqiNP_011004.3, NM_001178972.3

    Genome annotation databases

    EnsemblFungiiYER081W; YER081W; YER081W
    GeneIDi856814
    KEGGisce:YER081W

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18839 Genomic DNA Translation: AAB64636.1
    BK006939 Genomic DNA Translation: DAA07742.1
    PIRiS50584
    RefSeqiNP_011004.3, NM_001178972.3

    3D structure databases

    ProteinModelPortaliP40054
    SMRiP40054
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36826, 70 interactors
    DIPiDIP-5336N
    IntActiP40054, 7 interactors
    MINTiP40054
    STRINGi4932.YER081W

    Protein family/group databases

    MoonDBiP40054 Predicted

    PTM databases

    iPTMnetiP40054

    Proteomic databases

    MaxQBiP40054
    PaxDbiP40054
    PRIDEiP40054

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYER081W; YER081W; YER081W
    GeneIDi856814
    KEGGisce:YER081W

    Organism-specific databases

    SGDiS000000883 SER3

    Phylogenomic databases

    GeneTreeiENSGT00530000063021
    HOGENOMiHOG000136696
    InParanoidiP40054
    KOiK00058
    OMAiYHAIGIR
    OrthoDBiEOG092C2PBN

    Enzyme and pathway databases

    UniPathwayi
    UPA00135;UER00196

    BioCyciYEAST:YER081W-MONOMER
    ReactomeiR-SCE-977347 Serine biosynthesis

    Miscellaneous databases

    PROiPR:P40054

    Family and domain databases

    InterProiView protein in InterPro
    IPR002912 ACT_dom
    IPR006139 D-isomer_2_OHA_DH_cat_dom
    IPR029753 D-isomer_DH_CS
    IPR029752 D-isomer_DH_CS1
    IPR006140 D-isomer_DH_NAD-bd
    IPR036291 NAD(P)-bd_dom_sf
    IPR029015 PGDH_2
    PANTHERiPTHR10996:SF165 PTHR10996:SF165, 1 hit
    PfamiView protein in Pfam
    PF00389 2-Hacid_dh, 1 hit
    PF02826 2-Hacid_dh_C, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit
    PROSITEiView protein in PROSITE
    PS51671 ACT, 1 hit
    PS00065 D_2_HYDROXYACID_DH_1, 1 hit
    PS00670 D_2_HYDROXYACID_DH_2, 1 hit
    PS00671 D_2_HYDROXYACID_DH_3, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSERA_YEAST
    AccessioniPrimary (citable) accession number: P40054
    Secondary accession number(s): D3DLY8
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: November 7, 2018
    This is version 180 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names
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    Main funding by: National Institutes of Health

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