SERA2_ARATH
ID SERA2_ARATH Reviewed; 624 AA.
AC O04130; F4I918;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 2.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase 2, chloroplastic;
DE Short=PGDH;
DE EC=1.1.1.95 {ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856};
DE Flags: Precursor;
GN Name=PGDH2; Synonyms=3-PGDH, PGDH; OrderedLocusNames=At1g17745;
GN ORFNames=F11A6.8;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1), SUBCELLULAR LOCATION,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=9867856; DOI=10.1074/jbc.274.1.397;
RA Ho C.-L., Noji M., Saito M., Saito K.;
RT "Regulation of serine biosynthesis in Arabidopsis. Crucial role of
RT plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues.";
RL J. Biol. Chem. 274:397-402(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-71, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE,
RP AND INDUCTION BY CO(2) AND PATHOGEN.
RC STRAIN=cv. Columbia;
RX PubMed=24368794; DOI=10.1105/tpc.113.118992;
RA Benstein R.M., Ludewig K., Wulfert S., Wittek S., Gigolashvili T.,
RA Frerigmann H., Gierth M., Fluegge U.I., Krueger S.;
RT "Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway
RT is essential for development and required for ammonium assimilation and
RT tryptophan biosynthesis.";
RL Plant Cell 25:5011-5029(2013).
RN [11]
RP FUNCTION, GENE FAMILY, NOMENCLATURE, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=24058165; DOI=10.1104/pp.113.226720;
RA Toujani W., Munoz-Bertomeu J., Flores-Tornero M., Rosa-Tellez S.,
RA Anoman A.D., Alseekh S., Fernie A.R., Ros R.;
RT "Functional characterization of the plastidial 3-phosphoglycerate
RT dehydrogenase family in Arabidopsis.";
RL Plant Physiol. 163:1164-1178(2013).
CC -!- FUNCTION: Involved in the plastidial phosphorylated pathway of serine
CC biosynthesis (PPSB). {ECO:0000269|PubMed:24058165,
CC ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856}.
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:24368794, ECO:0000269|PubMed:9867856};
CC -!- ACTIVITY REGULATION: Inhibited by 90 uM 3-phosphonooxypyruvate, but not
CC by Ser, Thr, Val, Gly Trp, O-acetyl-L-Ser and Cys.
CC {ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.926 mM for 3-phospho-D-glycerate (at pH 7.2)
CC {ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856};
CC KM=0.899 mM for 3-phospho-D-glycerate (at pH 8.1)
CC {ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856};
CC KM=1.19 mM for 3-phospho-D-glycerate (at pH 9.0)
CC {ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856};
CC KM=0.271 mM for NAD(+) (at pH 7.2) {ECO:0000269|PubMed:24368794,
CC ECO:0000269|PubMed:9867856};
CC KM=0.189 mM for NAD(+) (at pH 8.1) {ECO:0000269|PubMed:24368794,
CC ECO:0000269|PubMed:9867856};
CC KM=0.01 mM for NAD(+) (at pH 9.0) {ECO:0000269|PubMed:24368794,
CC ECO:0000269|PubMed:9867856};
CC KM=0.35 mM for 3-phosphonooxypyruvate (at pH 7.1)
CC {ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856};
CC KM=0.12 mM for NADH (at pH 7.1) {ECO:0000269|PubMed:24368794,
CC ECO:0000269|PubMed:9867856};
CC Vmax=133 umol/min/mg enzyme (at pH 8.1) {ECO:0000269|PubMed:24368794,
CC ECO:0000269|PubMed:9867856};
CC Vmax=108 umol/min/mg enzyme (at pH 7.2) {ECO:0000269|PubMed:24368794,
CC ECO:0000269|PubMed:9867856};
CC -!- PATHWAY: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from
CC 3-phospho-D-glycerate: step 1/3.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:24058165, ECO:0000269|PubMed:24368794,
CC ECO:0000269|PubMed:9867856}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O04130-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O04130-2; Sequence=VSP_055873;
CC -!- TISSUE SPECIFICITY: Ubiquitous, but highly expressed in roots and in
CC dark-grown leaf tissues. Expressed in the vasculature, stigma, anther
CC filaments and shoot apical meristem. Not detected in the root meristem
CC or in embryo. {ECO:0000269|PubMed:24058165,
CC ECO:0000269|PubMed:24368794, ECO:0000269|PubMed:9867856}.
CC -!- INDUCTION: Not regulated by high CO(2) levels. Up-regulated upon
CC necrotrophic pathogen infection. {ECO:0000269|PubMed:24368794}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:24058165, ECO:0000269|PubMed:24368794}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; AB003280; BAA20405.1; -; mRNA.
DR EMBL; AB010407; BAA24440.1; -; Genomic_DNA.
DR EMBL; AC034257; AAF99816.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29630.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29631.1; -; Genomic_DNA.
DR EMBL; AY050399; AAK91415.1; -; mRNA.
DR EMBL; AY098953; AAM19963.1; -; mRNA.
DR EMBL; AY086001; AAM63210.1; -; mRNA.
DR PIR; T52296; T52296.
DR RefSeq; NP_001031061.2; NM_001035984.2. [O04130-2]
DR RefSeq; NP_564034.1; NM_101636.3. [O04130-1]
DR AlphaFoldDB; O04130; -.
DR SMR; O04130; -.
DR BioGRID; 23591; 12.
DR IntAct; O04130; 1.
DR STRING; 3702.AT1G17745.2; -.
DR iPTMnet; O04130; -.
DR PaxDb; O04130; -.
DR PRIDE; O04130; -.
DR ProteomicsDB; 232830; -. [O04130-1]
DR EnsemblPlants; AT1G17745.1; AT1G17745.1; AT1G17745. [O04130-1]
DR EnsemblPlants; AT1G17745.2; AT1G17745.2; AT1G17745. [O04130-2]
DR GeneID; 838352; -.
DR Gramene; AT1G17745.1; AT1G17745.1; AT1G17745. [O04130-1]
DR Gramene; AT1G17745.2; AT1G17745.2; AT1G17745. [O04130-2]
DR KEGG; ath:AT1G17745; -.
DR Araport; AT1G17745; -.
DR TAIR; locus:505006128; AT1G17745.
DR eggNOG; KOG0068; Eukaryota.
DR HOGENOM; CLU_019796_8_1_1; -.
DR InParanoid; O04130; -.
DR OMA; EAIMAIG; -.
DR OrthoDB; 911009at2759; -.
DR PhylomeDB; O04130; -.
DR BioCyc; ARA:AT1G17745-MON; -.
DR BioCyc; MetaCyc:AT1G17745-MON; -.
DR BRENDA; 1.1.1.95; 399.
DR SABIO-RK; O04130; -.
DR UniPathway; UPA00135; UER00196.
DR PRO; PR:O04130; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; O04130; baseline and differential.
DR Genevisible; O04130; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0006564; P:L-serine biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1330.90; -; 1.
DR InterPro; IPR045865; ACT-like_dom_sf.
DR InterPro; IPR002912; ACT_dom.
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; PF01842; ACT; 1.
DR Pfam; PF19304; PGDH_inter; 1.
DR SUPFAM; SSF143548; SSF143548; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF55021; SSF55021; 1.
DR TIGRFAMs; TIGR01327; PGDH; 1.
DR PROSITE; PS51671; ACT; 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 Alternative splicing; Amino-acid biosynthesis; Chloroplast; NAD;
KW Oxidoreductase; Phosphoprotein; Plastid; Reference proteome;
KW Serine biosynthesis; Transit peptide.
FT TRANSIT 1..49
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 50..624
FT /note="D-3-phosphoglycerate dehydrogenase 2, chloroplastic"
FT /id="PRO_0000007192"
FT DOMAIN 552..624
FT /note="ACT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01007"
FT ACT_SITE 312
FT /evidence="ECO:0000250"
FT ACT_SITE 341
FT /evidence="ECO:0000250"
FT ACT_SITE 360
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 231..232
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 251
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 310..312
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 336
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 360..363
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT MOD_RES 71
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157"
FT VAR_SEQ 208..210
FT /note="KWE -> TLNYLFLVLLLRWNCRQSKHQYTIETETEK (in isoform
FT 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_055873"
SQ SEQUENCE 624 AA; 66454 MW; 724370F870DEA310 CRC64;
MAFSSSCSSV KAVNSRWTSP SPSPSSRFAV LPAFLHRRYA TSVKLTAISA ALKTVEQTTL
TEDNRFSTVG SDSDEYNPTL PKPRILVTEK LGEAGVNLLR EFGDVDCSYD LSPEDLKKKV
AESDALIVRS GTKVTREVFE AAKGRLKVVG RAGVGIDNVD LQAATEHGCL VVNAPTANTV
AAAEHGIALL ASMARNVAQA DASIKAGKWE RSKYVGVSLV GKTLAVMGFG KVGTEVARRA
KGLGMTVISH DPYAPADRAR ALGVDLVSFD QAISTADFVS LHMPLTPATK KVFNDETFSK
MKKGVRLINV ARGGVIDEDA LVRALDAGIV AQAALDVFCE EPPSKDSRLI QHENVTVTPH
LGASTKEAQE GVAIEIAEAV AGALKGELSA TAVNAPMVAP EVLSELTPYI VLAEKLGRLA
VQLASGGKGV QSIRVVYRSA RDRDDLDTRL LRAMITKGII EPISDSYVNL VNADFIAKQK
GLRISEERMV VDSSPEYPVD SIQVQILNVE SNFAGAVSDA GDISIEGKVK YGVPHLTCVG
SFGVDVSLEG NLILCRQVDQ PGMIGQVGNI LGEQNVNVNF MSVGRTVLRK QAIMAIGVDE
EPDNKTLERI GGVSAIEEFV FLKL
