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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: Annotation score: 5 out of 5-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 1 (SER3), D-3-phosphoglycerate dehydrogenase 2 (SER33)
    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
    • amino acid binding Source: InterPro
    • identical protein binding Source: IntAct
    • NAD binding Source: InterPro
    • phosphoglycerate dehydrogenase activity Source: SGD

    GO - Biological processi

    • L-serine biosynthetic process Source: UniProtKB-KW
    • serine family amino acid biosynthetic process Source: SGD

    Keywordsi

    Molecular functionOxidoreductase
    Biological processAmino-acid biosynthesis, Serine biosynthesis
    LigandNAD

    Enzyme and pathway databases

    BioCyciYEAST:YER081W-MONOMER.
    ReactomeiR-SCE-977347. Serine biosynthesis.
    UniPathwayiUPA00135; UER00196.

    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

    EuPathDBiFungiDB:YER081W.
    SGDiS000000883. SER3.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemovedBy similarity
    ChainiPRO_00000760182 – 469D-3-phosphoglycerate dehydrogenase 1Add BLAST468

    Amino acid modifications

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

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP40054.
    PRIDEiP40054.

    PTM databases

    iPTMnetiP40054.

    Interactioni

    Binary interactionsi

    Show more details

    GO - Molecular functioni

    • identical protein binding Source: IntAct

    Protein-protein interaction databases

    BioGridi36826. 65 interactors.
    DIPiDIP-5336N.
    IntActiP40054. 21 interactors.
    MINTiMINT-404076.

    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

    GeneTreeiENSGT00840000129939.
    HOGENOMiHOG000136696.
    InParanoidiP40054.
    KOiK00058.
    OMAiAIDEDHV.
    OrthoDBiEOG092C2PBN.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    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.
    IPR016040. NAD(P)-bd_dom.
    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    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.

    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. 65 interactors.
    DIPiDIP-5336N.
    IntActiP40054. 21 interactors.
    MINTiMINT-404076.

    PTM databases

    iPTMnetiP40054.

    Proteomic databases

    MaxQBiP40054.
    PRIDEiP40054.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYER081W; YER081W; YER081W.
    GeneIDi856814.
    KEGGisce:YER081W.

    Organism-specific databases

    EuPathDBiFungiDB:YER081W.
    SGDiS000000883. SER3.

    Phylogenomic databases

    GeneTreeiENSGT00840000129939.
    HOGENOMiHOG000136696.
    InParanoidiP40054.
    KOiK00058.
    OMAiAIDEDHV.
    OrthoDBiEOG092C2PBN.

    Enzyme and pathway databases

    UniPathwayiUPA00135; UER00196.
    BioCyciYEAST:YER081W-MONOMER.
    ReactomeiR-SCE-977347. Serine biosynthesis.

    Miscellaneous databases

    PROiPR:P40054.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    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.
    IPR016040. NAD(P)-bd_dom.
    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: March 15, 2017
    This is version 165 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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 V
      Yeast (Saccharomyces cerevisiae) chromosome V: 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.