SERA_MOUSE
ID SERA_MOUSE Reviewed; 533 AA.
AC Q61753; Q3TEE5; Q75SV9; Q8C603;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase;
DE Short=3-PGDH;
DE EC=1.1.1.95 {ECO:0000250|UniProtKB:O08651};
DE AltName: Full=A10;
GN Name=Phgdh;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=129/SvJ;
RX PubMed=14645240; DOI=10.1074/jbc.c300507200;
RA Yoshida K., Furuya S., Osuka S., Mitoma J., Shinoda Y., Watanabe M.,
RA Azuma N., Tanaka H., Hashikawa T., Itohara S., Hirabayashi Y.;
RT "Targeted disruption of the mouse 3-phosphoglycerate dehydrogenase gene
RT causes severe neurodevelopmental defects and results in embryonic
RT lethality.";
RL J. Biol. Chem. 279:3573-3577(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J, and NOD; TISSUE=Testis, and Thymus;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Brain, and Olfactory epithelium;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP PROTEIN SEQUENCE OF 39-54; 248-268; 365-380 AND 523-533, AND IDENTIFICATION
RP BY MASS SPECTROMETRY.
RC TISSUE=Brain, and Hippocampus;
RA Lubec G., Klug S., Yang J.W., Zigmond M.;
RL Submitted (JUL-2007) to UniProtKB.
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 49-533.
RA Miller I.J., Bieker J.J.;
RT "Sequences and expression patterns of murine erythroleukemia cDNAs isolated
RT by subtractive cloning.";
RL Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP DISRUPTION PHENOTYPE.
RX PubMed=19114063; DOI=10.1016/j.neures.2008.12.002;
RA Kawakami Y., Yoshida K., Yang J.H., Suzuki T., Azuma N., Sakai K.,
RA Hashikawa T., Watanabe M., Yasuda K., Kuhara S., Hirabayashi Y., Furuya S.;
RT "Impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a
RT serine deficiency disorder model.";
RL Neurosci. Res. 63:184-193(2009).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-78, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-21 AND LYS-58, AND IDENTIFICATION
RP BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=23806337; DOI=10.1016/j.molcel.2013.06.001;
RA Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y.,
RA Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.;
RT "SIRT5-mediated lysine desuccinylation impacts diverse metabolic
RT pathways.";
RL Mol. Cell 50:919-930(2013).
CC -!- FUNCTION: Catalyzes the reversible oxidation of 3-phospho-D-glycerate
CC to 3-phosphonooxypyruvate, the first step of the phosphorylated L-
CC serine biosynthesis pathway. Does not catalyze the reversible oxidation
CC of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of
CC (S)-malate to oxaloacetate. {ECO:0000250|UniProtKB:O08651}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + H(+)
CC + NADH; Xref=Rhea:RHEA:12641, ChEBI:CHEBI:15378, ChEBI:CHEBI:18110,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:58272; EC=1.1.1.95;
CC Evidence={ECO:0000250|UniProtKB:O08651};
CC -!- PATHWAY: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from
CC 3-phospho-D-glycerate: step 1/3.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250|UniProtKB:O08651}.
CC -!- DISRUPTION PHENOTYPE: Decreased level of free serine, glycine, taurine,
CC GABA, glutamine, and threonine in spinal cord and head. Impaired
CC central nervous system (CNS) with shorter neural tube length and
CC overall growth retardation. Severe atrophy at the thoracic level,
CC particularly in the dorsal spinal cord. Poorly developed dorsal horn
CC and adjacent mantle zone. Neurons fail to develop neurites,
CC particularly commissural axonal fibers. {ECO:0000269|PubMed:19114063}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; AB128936; BAD08449.1; -; Genomic_DNA.
DR EMBL; AK076815; BAC36494.1; -; mRNA.
DR EMBL; AK169684; BAE41303.1; -; mRNA.
DR EMBL; BC086668; AAH86668.1; -; mRNA.
DR EMBL; BC110673; AAI10674.1; -; mRNA.
DR EMBL; L21027; AAB67986.1; -; mRNA.
DR CCDS; CCDS17663.1; -.
DR RefSeq; NP_058662.2; NM_016966.3.
DR AlphaFoldDB; Q61753; -.
DR SMR; Q61753; -.
DR BioGRID; 231770; 19.
DR IntAct; Q61753; 9.
DR MINT; Q61753; -.
DR STRING; 10090.ENSMUSP00000064755; -.
DR iPTMnet; Q61753; -.
DR PhosphoSitePlus; Q61753; -.
DR SwissPalm; Q61753; -.
DR COMPLUYEAST-2DPAGE; Q61753; -.
DR REPRODUCTION-2DPAGE; IPI00225961; -.
DR REPRODUCTION-2DPAGE; Q61753; -.
DR SWISS-2DPAGE; Q61753; -.
DR EPD; Q61753; -.
DR jPOST; Q61753; -.
DR MaxQB; Q61753; -.
DR PaxDb; Q61753; -.
DR PeptideAtlas; Q61753; -.
DR PRIDE; Q61753; -.
DR ProteomicsDB; 256964; -.
DR Antibodypedia; 3291; 484 antibodies from 35 providers.
DR DNASU; 236539; -.
DR Ensembl; ENSMUST00000065793; ENSMUSP00000064755; ENSMUSG00000053398.
DR GeneID; 236539; -.
DR KEGG; mmu:236539; -.
DR UCSC; uc008qps.1; mouse.
DR CTD; 26227; -.
DR MGI; MGI:1355330; Phgdh.
DR VEuPathDB; HostDB:ENSMUSG00000053398; -.
DR eggNOG; KOG0068; Eukaryota.
DR GeneTree; ENSGT00940000155863; -.
DR HOGENOM; CLU_019796_8_1_1; -.
DR InParanoid; Q61753; -.
DR OMA; NIAGMQV; -.
DR OrthoDB; 911009at2759; -.
DR PhylomeDB; Q61753; -.
DR TreeFam; TF314548; -.
DR BRENDA; 1.1.1.95; 3474.
DR Reactome; R-MMU-977347; Serine biosynthesis.
DR UniPathway; UPA00135; UER00196.
DR BioGRID-ORCS; 236539; 3 hits in 74 CRISPR screens.
DR ChiTaRS; Phgdh; mouse.
DR PRO; PR:Q61753; -.
DR Proteomes; UP000000589; Chromosome 3.
DR RNAct; Q61753; protein.
DR Bgee; ENSMUSG00000053398; Expressed in ventricular zone and 235 other tissues.
DR ExpressionAtlas; Q61753; baseline and differential.
DR Genevisible; Q61753; MM.
DR GO; GO:0043209; C:myelin sheath; HDA:UniProtKB.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; ISO:MGI.
DR GO; GO:0070314; P:G1 to G0 transition; IMP:MGI.
DR GO; GO:0009448; P:gamma-aminobutyric acid metabolic process; IMP:MGI.
DR GO; GO:0021782; P:glial cell development; IMP:MGI.
DR GO; GO:0006541; P:glutamine metabolic process; IMP:MGI.
DR GO; GO:0006544; P:glycine metabolic process; IMP:MGI.
DR GO; GO:0006564; P:L-serine biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0006563; P:L-serine metabolic process; IMP:MGI.
DR GO; GO:0021915; P:neural tube development; IMP:MGI.
DR GO; GO:0022008; P:neurogenesis; IMP:MGI.
DR GO; GO:0031175; P:neuron projection development; IMP:MGI.
DR GO; GO:0010468; P:regulation of gene expression; IMP:MGI.
DR GO; GO:0021510; P:spinal cord development; IMP:MGI.
DR GO; GO:0019530; P:taurine metabolic process; IMP:MGI.
DR GO; GO:0006566; P:threonine metabolic process; IMP:MGI.
DR Gene3D; 3.30.1330.90; -; 1.
DR InterPro; IPR029009; ASB_dom_sf.
DR InterPro; IPR006139; D-isomer_2_OHA_DH_cat_dom.
DR InterPro; IPR029753; D-isomer_DH_CS.
DR InterPro; IPR029752; D-isomer_DH_CS1.
DR InterPro; IPR006140; D-isomer_DH_NAD-bd.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR006236; PGDH.
DR InterPro; IPR045626; PGDH_ASB_dom.
DR Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR Pfam; PF19304; PGDH_inter; 1.
DR SUPFAM; SSF143548; SSF143548; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01327; PGDH; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
DR PROSITE; PS00670; D_2_HYDROXYACID_DH_2; 1.
DR PROSITE; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 1: Evidence at protein level;
KW Acetylation; Amino-acid biosynthesis; Direct protein sequencing;
KW Isopeptide bond; NAD; Oxidoreductase; Phosphoprotein; Reference proteome;
KW Serine biosynthesis; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT CHAIN 2..533
FT /note="D-3-phosphoglycerate dehydrogenase"
FT /id="PRO_0000076014"
FT ACT_SITE 236
FT /evidence="ECO:0000250"
FT ACT_SITE 265
FT /evidence="ECO:0000250"
FT ACT_SITE 283
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 78
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT BINDING 155..156
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT BINDING 207
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT BINDING 234..236
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT BINDING 260
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT BINDING 283..286
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT MOD_RES 14
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT MOD_RES 21
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0007744|PubMed:23806337"
FT MOD_RES 58
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:23806337"
FT MOD_RES 78
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT CROSSLNK 21
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO1); alternate"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT CROSSLNK 21
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2); alternate"
FT /evidence="ECO:0000250|UniProtKB:O43175"
FT CONFLICT 77
FT /note="G -> V (in Ref. 5; AAB67986)"
FT /evidence="ECO:0000305"
FT CONFLICT 87..88
FT /note="AA -> PP (in Ref. 5; AAB67986)"
FT /evidence="ECO:0000305"
FT CONFLICT 124
FT /note="A -> T (in Ref. 5; AAB67986)"
FT /evidence="ECO:0000305"
FT CONFLICT 369
FT /note="C -> W (in Ref. 5; AAB67986)"
FT /evidence="ECO:0000305"
FT CONFLICT 377
FT /note="G -> A (in Ref. 5; AAB67986)"
FT /evidence="ECO:0000305"
FT CONFLICT 447
FT /note="M -> K (in Ref. 2; BAC36494)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 533 AA; 56586 MW; 49CBF125AD6A12A5 CRC64;
MAFANLRKVL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG LIVRSATKVT
ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN GNSLSAAELT CGMIMCLARQ
IPQATASMKD GKWDRKKFMG TELNGKTLGI LGLGRIGREV ATRMQSFGMK TVGYDPIISP
EVAASFGVQQ LPLEEIWPLC DFITVHTPLL PSTTGLLNDS TFAQCKKGVR VVNCARGGIV
DEGALLRALQ SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEAMG TLMHAWAGSP KGTIQVVTQG
TSLKNAGTCL SPAVIVGLLR EASKQADVNL VNAKLLVKEA GLNVTTSHNP GVPGEQGSGE
CLLTVALAGA PYQAVGLVQG TTPMLQMLNG AVFRPEVPLR RGQPLLVFRA QPSDPGMLPT
MIGLLAEAGV QLLSYQTSMV SDGEPWHVMG LSSLLPSLET WKQHVLEAFQ FCF
