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Q61753

- SERA_MOUSE

UniProt

Q61753 - SERA_MOUSE

Protein

D-3-phosphoglycerate dehydrogenase

Gene

Phgdh

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.
    2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei78 – 781NADBy similarity
    Binding sitei175 – 1751NADBy similarity
    Binding sitei207 – 2071NAD; via carbonyl oxygenBy similarity
    Active sitei236 – 2361By similarity
    Binding sitei260 – 2601NADBy similarity
    Active sitei265 – 2651By similarity
    Active sitei283 – 2831Proton donorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi155 – 1562NADBy similarity
    Nucleotide bindingi234 – 2363NADBy similarity
    Nucleotide bindingi283 – 2864NADBy similarity

    GO - Molecular functioni

    1. NAD binding Source: InterPro
    2. phosphoglycerate dehydrogenase activity Source: MGI

    GO - Biological processi

    1. G1 to G0 transition Source: MGI
    2. gamma-aminobutyric acid metabolic process Source: MGI
    3. glial cell development Source: MGI
    4. glutamine metabolic process Source: MGI
    5. glycine metabolic process Source: MGI
    6. L-serine biosynthetic process Source: UniProtKB-KW
    7. L-serine metabolic process Source: MGI
    8. neural tube development Source: MGI
    9. neurogenesis Source: MGI
    10. neuron projection development Source: MGI
    11. regulation of gene expression Source: MGI
    12. spinal cord development Source: MGI
    13. taurine metabolic process Source: MGI
    14. threonine metabolic process Source: MGI

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Serine biosynthesis

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    ReactomeiREACT_199119. Serine biosynthesis.
    UniPathwayiUPA00135; UER00196.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-3-phosphoglycerate dehydrogenase (EC:1.1.1.95)
    Short name:
    3-PGDH
    Alternative name(s):
    A10
    Gene namesi
    Name:Phgdh
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 3

    Organism-specific databases

    MGIiMGI:1355330. Phgdh.

    Pathology & Biotechi

    Disruption phenotypei

    Decreased level of free serine, glycine, taurine, GABA, glutamine, and threonine in spinal cord and head. Impaired central nervous system (CNS) with shorter neural tube length and overall growth retardation. Severe atrophy at the thoracic level, particularly in the dorsal spinal cord. Poorly developed dorsal horn and adjacent mantle zone. Neurons fail to develop neurites, particularly commissural axonal fibers.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 533532D-3-phosphoglycerate dehydrogenasePRO_0000076014Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanineBy similarity
    Modified residuei21 – 211N6-acetyllysine1 Publication
    Modified residuei58 – 581N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiQ61753.
    PaxDbiQ61753.
    PRIDEiQ61753.

    2D gel databases

    COMPLUYEAST-2DPAGEQ61753.
    REPRODUCTION-2DPAGEIPI00225961.
    Q61753.
    SWISS-2DPAGEQ61753.

    PTM databases

    PhosphoSiteiQ61753.

    Expressioni

    Gene expression databases

    BgeeiQ61753.
    CleanExiMM_PHGDH.
    GenevestigatoriQ61753.

    Interactioni

    Subunit structurei

    Homotetramer.By similarity

    Protein-protein interaction databases

    BioGridi231770. 2 interactions.
    IntActiQ61753. 4 interactions.
    MINTiMINT-4114515.

    Structurei

    3D structure databases

    ProteinModelPortaliQ61753.
    SMRiQ61753. Positions 5-503.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0111.
    GeneTreeiENSGT00530000063021.
    HOGENOMiHOG000136693.
    HOVERGENiHBG054241.
    InParanoidiQ61753.
    KOiK00058.
    OMAiDNTFAQC.
    OrthoDBiEOG7JT6WT.
    PhylomeDBiQ61753.
    TreeFamiTF314548.

    Family and domain databases

    Gene3Di3.30.1330.90. 1 hit.
    3.40.50.720. 2 hits.
    InterProiIPR029009. ASB_dom.
    IPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    IPR006236. PGDH.
    [Graphical view]
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF143548. SSF143548. 1 hit.
    TIGRFAMsiTIGR01327. PGDH. 1 hit.
    PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q61753-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAFANLRKVL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG    50
    LIVRSATKVT ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN 100
    GNSLSAAELT CGMIMCLARQ IPQATASMKD GKWDRKKFMG TELNGKTLGI 150
    LGLGRIGREV ATRMQSFGMK TVGYDPIISP EVAASFGVQQ LPLEEIWPLC 200
    DFITVHTPLL PSTTGLLNDS TFAQCKKGVR VVNCARGGIV DEGALLRALQ 250
    SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA 300
    VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEAMG TLMHAWAGSP 350
    KGTIQVVTQG TSLKNAGTCL SPAVIVGLLR EASKQADVNL VNAKLLVKEA 400
    GLNVTTSHNP GVPGEQGSGE CLLTVALAGA PYQAVGLVQG TTPMLQMLNG 450
    AVFRPEVPLR RGQPLLVFRA QPSDPGMLPT MIGLLAEAGV QLLSYQTSMV 500
    SDGEPWHVMG LSSLLPSLET WKQHVLEAFQ FCF 533
    Length:533
    Mass (Da):56,586
    Last modified:January 23, 2007 - v3
    Checksum:i49CBF125AD6A12A5
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti77 – 771G → V in AAB67986. 1 PublicationCurated
    Sequence conflicti87 – 882AA → PP in AAB67986. 1 PublicationCurated
    Sequence conflicti124 – 1241A → T in AAB67986. 1 PublicationCurated
    Sequence conflicti369 – 3691C → W in AAB67986. 1 PublicationCurated
    Sequence conflicti377 – 3771G → A in AAB67986. 1 PublicationCurated
    Sequence conflicti447 – 4471M → K in BAC36494. (PubMed:16141072)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB128936 Genomic DNA. Translation: BAD08449.1.
    AK076815 mRNA. Translation: BAC36494.1.
    AK169684 mRNA. Translation: BAE41303.1.
    BC086668 mRNA. Translation: AAH86668.1.
    BC110673 mRNA. Translation: AAI10674.1.
    L21027 mRNA. Translation: AAB67986.1.
    CCDSiCCDS17663.1.
    RefSeqiNP_058662.2. NM_016966.3.
    UniGeneiMm.16898.
    Mm.371997.

    Genome annotation databases

    EnsembliENSMUST00000065793; ENSMUSP00000064755; ENSMUSG00000053398.
    GeneIDi236539.
    KEGGimmu:236539.
    UCSCiuc008qps.1. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB128936 Genomic DNA. Translation: BAD08449.1 .
    AK076815 mRNA. Translation: BAC36494.1 .
    AK169684 mRNA. Translation: BAE41303.1 .
    BC086668 mRNA. Translation: AAH86668.1 .
    BC110673 mRNA. Translation: AAI10674.1 .
    L21027 mRNA. Translation: AAB67986.1 .
    CCDSi CCDS17663.1.
    RefSeqi NP_058662.2. NM_016966.3.
    UniGenei Mm.16898.
    Mm.371997.

    3D structure databases

    ProteinModelPortali Q61753.
    SMRi Q61753. Positions 5-503.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 231770. 2 interactions.
    IntActi Q61753. 4 interactions.
    MINTi MINT-4114515.

    PTM databases

    PhosphoSitei Q61753.

    2D gel databases

    COMPLUYEAST-2DPAGE Q61753.
    REPRODUCTION-2DPAGE IPI00225961.
    Q61753.
    SWISS-2DPAGE Q61753.

    Proteomic databases

    MaxQBi Q61753.
    PaxDbi Q61753.
    PRIDEi Q61753.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000065793 ; ENSMUSP00000064755 ; ENSMUSG00000053398 .
    GeneIDi 236539.
    KEGGi mmu:236539.
    UCSCi uc008qps.1. mouse.

    Organism-specific databases

    CTDi 26227.
    MGIi MGI:1355330. Phgdh.

    Phylogenomic databases

    eggNOGi COG0111.
    GeneTreei ENSGT00530000063021.
    HOGENOMi HOG000136693.
    HOVERGENi HBG054241.
    InParanoidi Q61753.
    KOi K00058.
    OMAi DNTFAQC.
    OrthoDBi EOG7JT6WT.
    PhylomeDBi Q61753.
    TreeFami TF314548.

    Enzyme and pathway databases

    UniPathwayi UPA00135 ; UER00196 .
    Reactomei REACT_199119. Serine biosynthesis.

    Miscellaneous databases

    NextBioi 382995.
    PROi Q61753.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q61753.
    CleanExi MM_PHGDH.
    Genevestigatori Q61753.

    Family and domain databases

    Gene3Di 3.30.1330.90. 1 hit.
    3.40.50.720. 2 hits.
    InterProi IPR029009. ASB_dom.
    IPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    IPR006236. PGDH.
    [Graphical view ]
    Pfami PF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF143548. SSF143548. 1 hit.
    TIGRFAMsi TIGR01327. PGDH. 1 hit.
    PROSITEi PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Targeted disruption of the mouse 3-phosphoglycerate dehydrogenase gene causes severe neurodevelopmental defects and results in embryonic lethality."
      Yoshida K., Furuya S., Osuka S., Mitoma J., Shinoda Y., Watanabe M., Azuma N., Tanaka H., Hashikawa T., Itohara S., Hirabayashi Y.
      J. Biol. Chem. 279:3573-3577(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 129/SvJ.
    2. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6J and NOD.
      Tissue: Testis and Thymus.
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6.
      Tissue: Brain and Olfactory epithelium.
    4. Lubec G., Klug S., Yang J.W., Zigmond M.
      Submitted (JUL-2007) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 39-54; 248-268; 365-380 AND 523-533, IDENTIFICATION BY MASS SPECTROMETRY.
      Tissue: Brain and Hippocampus.
    5. "Sequences and expression patterns of murine erythroleukemia cDNAs isolated by subtractive cloning."
      Miller I.J., Bieker J.J.
      Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 49-533.
    6. "Impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a serine deficiency disorder model."
      Kawakami Y., Yoshida K., Yang J.H., Suzuki T., Azuma N., Sakai K., Hashikawa T., Watanabe M., Yasuda K., Kuhara S., Hirabayashi Y., Furuya S.
      Neurosci. Res. 63:184-193(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
    7. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
      Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
      Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-21 AND LYS-58, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Embryonic fibroblast.

    Entry informationi

    Entry nameiSERA_MOUSE
    AccessioniPrimary (citable) accession number: Q61753
    Secondary accession number(s): Q3TEE5, Q75SV9, Q8C603
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 130 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3