SERA_RAT
ID SERA_RAT Reviewed; 533 AA.
AC O08651; Q546Q9;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase;
DE Short=3-PGDH;
DE EC=1.1.1.95 {ECO:0000269|PubMed:9163325};
GN Name=Phgdh;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], SUBUNIT, TISSUE SPECIFICITY, FUNCTION,
RP CATALYTIC ACTIVITY, AND PATHWAY.
RX PubMed=9163325; DOI=10.1042/bj3230365;
RA Achouri Y., Rider M.H., van Schaftingen E., Robbi M.;
RT "Cloning, sequencing and expression of rat liver 3-phosphoglycerate
RT dehydrogenase.";
RL Biochem. J. 323:365-370(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Robbi M., Achouri Y., Szpirer C., Van Schaftingen E.;
RT "Structure and chromosomal localization of the rat gene encoding 3-
RT phosphoglycerate dehydrogenase.";
RL Submitted (FEB-2000) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Testis;
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 34-54; 248-270; 271-289 AND 365-380, AND IDENTIFICATION
RP BY MASS SPECTROMETRY.
RC STRAIN=Sprague-Dawley; TISSUE=Spinal cord;
RA Lubec G., Afjehi-Sadat L.;
RL Submitted (NOV-2006) to UniProtKB.
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:0000269|PubMed:9163325}.
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:0000269|PubMed:9163325};
CC -!- PATHWAY: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from
CC 3-phospho-D-glycerate: step 1/3. {ECO:0000269|PubMed:9163325}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:9163325}.
CC -!- TISSUE SPECIFICITY: Liver, kidney, brain, testis.
CC {ECO:0000269|PubMed:9163325}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; X97772; CAA66374.1; -; mRNA.
DR EMBL; AJ271975; CAB89828.1; -; Genomic_DNA.
DR EMBL; BC086327; AAH86327.1; -; mRNA.
DR RefSeq; NP_113808.1; NM_031620.1.
DR RefSeq; XP_006233072.1; XM_006233010.1.
DR AlphaFoldDB; O08651; -.
DR SMR; O08651; -.
DR BioGRID; 248638; 2.
DR IntAct; O08651; 2.
DR MINT; O08651; -.
DR STRING; 10116.ENSRNOP00000053019; -.
DR iPTMnet; O08651; -.
DR PhosphoSitePlus; O08651; -.
DR SwissPalm; O08651; -.
DR World-2DPAGE; 0004:O08651; -.
DR jPOST; O08651; -.
DR PaxDb; O08651; -.
DR PRIDE; O08651; -.
DR GeneID; 58835; -.
DR KEGG; rno:58835; -.
DR UCSC; RGD:61987; rat.
DR CTD; 26227; -.
DR RGD; 61987; Phgdh.
DR VEuPathDB; HostDB:ENSRNOG00000019328; -.
DR eggNOG; KOG0068; Eukaryota.
DR HOGENOM; CLU_019796_8_1_1; -.
DR InParanoid; O08651; -.
DR OMA; NIAGMQV; -.
DR OrthoDB; 911009at2759; -.
DR PhylomeDB; O08651; -.
DR TreeFam; TF314548; -.
DR BioCyc; MetaCyc:MON-10261; -.
DR Reactome; R-RNO-977347; Serine biosynthesis.
DR UniPathway; UPA00135; UER00196.
DR PRO; PR:O08651; -.
DR Proteomes; UP000002494; Chromosome 2.
DR Bgee; ENSRNOG00000019328; Expressed in pancreas and 19 other tissues.
DR Genevisible; O08651; RN.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IDA:RGD.
DR GO; GO:0070314; P:G1 to G0 transition; ISO:RGD.
DR GO; GO:0009448; P:gamma-aminobutyric acid metabolic process; ISO:RGD.
DR GO; GO:0021782; P:glial cell development; ISO:RGD.
DR GO; GO:0006541; P:glutamine metabolic process; ISO:RGD.
DR GO; GO:0006544; P:glycine metabolic process; ISO:RGD.
DR GO; GO:0006564; P:L-serine biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0006563; P:L-serine metabolic process; ISO:RGD.
DR GO; GO:0021915; P:neural tube development; ISO:RGD.
DR GO; GO:0022008; P:neurogenesis; ISO:RGD.
DR GO; GO:0031175; P:neuron projection development; ISO:RGD.
DR GO; GO:0010468; P:regulation of gene expression; ISO:RGD.
DR GO; GO:0009070; P:serine family amino acid biosynthetic process; TAS:RGD.
DR GO; GO:0021510; P:spinal cord development; ISO:RGD.
DR GO; GO:0019530; P:taurine metabolic process; ISO:RGD.
DR GO; GO:0006566; P:threonine metabolic process; ISO:RGD.
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_0000076016"
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:0000250|UniProtKB:Q61753"
FT MOD_RES 58
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q61753"
FT MOD_RES 78
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:O43175"
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"
SQ SEQUENCE 533 AA; 56493 MW; 7273DAC3349E95EF CRC64;
MAFANLRKIL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG LIVRSATKVT
ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGVLVMNTPN GNSLSAAELT CGMLMCLARQ
IPQATASMKD GKWDRKKFMG TELNGKTLGI LGLGRIGREV AARMQAFGMK TVGYDPIISP
EVAASFGVQQ LPLEEIWPLC DFITVHTPLL PSTTGLLNDS TFAQCKKGVR VVNCARGGIV
DEGALLRALQ SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEALG TLMHAWAGSP KGTIQVVTQG
TSLKNAGTCL SPAVIVGLLR EASKQADVNL VNAKLLVKEA GLNVTTSHSP GVPGEQGIGE
CLLTVALAGA PYQAVGLVQG TTPMLQMLNG AVFRPEVPLR RGQPLLLFRA QPSDPVMLPT
MIGLLAEAGV QLLSYQTSKV SDGDTWHVMG LSSLLPSLDA WKQHVSEAFQ FCF
