SERA1_ARATH
ID SERA1_ARATH Reviewed; 603 AA.
AC O49485; Q8LGJ6;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase 1, chloroplastic;
DE EC=1.1.1.95 {ECO:0000269|PubMed:24368794};
DE AltName: Full=Protein EMBRYO SAC DEVELOPMENT ARREST 9;
DE Flags: Precursor;
GN Name=PGDH1; Synonyms=EDA9; OrderedLocusNames=At4g34200; ORFNames=F10M10.7;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [5]
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 [6]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR
RP LOCATION, ACTIVITY REGULATION, 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 [7]
RP FUNCTION, GENE FAMILY, NOMENCLATURE, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, INDUCTION, 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). Required for mature pollen development.
CC {ECO:0000269|PubMed:24058165, ECO:0000269|PubMed:24368794}.
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};
CC -!- ACTIVITY REGULATION: Partially inhibited by 5 mM serine.
CC {ECO:0000269|PubMed:24368794}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.308 mM for 3-phospho-D-glycerate (at pH 8.1)
CC {ECO:0000269|PubMed:24368794};
CC KM=0.39 mM for NAD(+) (at pH 8.1) {ECO:0000269|PubMed:24368794};
CC KM=2.11 mM for 3-phospho-D-glycerate (at pH 7.2)
CC {ECO:0000269|PubMed:24368794};
CC KM=0.377 mM for NAD(+) (at pH 7.2) {ECO:0000269|PubMed:24368794};
CC Vmax=165 umol/min/mg enzyme (at pH 8.1)
CC {ECO:0000269|PubMed:24368794};
CC Vmax=109.1 umol/min/mg enzyme (at pH 7.2)
CC {ECO:0000269|PubMed:24368794};
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 -!- TISSUE SPECIFICITY: Ubiquitous, but highly expressed in roots.
CC Expressed in vasculature, root and shoot meristems, distal part of
CC cotyledons and leaves, anther, stigma and pollen grains. Detected at
CC the tip of the cotyledons in late embryos.
CC {ECO:0000269|PubMed:24058165, ECO:0000269|PubMed:24368794}.
CC -!- INDUCTION: Up-regulated in the aerial parts by dark treatment, high
CC CO(2) levels and necrotrophic pathogen infection.
CC {ECO:0000269|PubMed:24058165, ECO:0000269|PubMed:24368794}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethal when homozygous.
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; AL021961; CAA17552.1; -; Genomic_DNA.
DR EMBL; AL161585; CAB80137.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86339.1; -; Genomic_DNA.
DR EMBL; AY063810; AAL36166.1; -; mRNA.
DR EMBL; AY150462; AAN12903.1; -; mRNA.
DR EMBL; AY084236; AAM60833.1; -; mRNA.
DR PIR; T05416; T05416.
DR RefSeq; NP_195146.1; NM_119583.4.
DR AlphaFoldDB; O49485; -.
DR SMR; O49485; -.
DR BioGRID; 14850; 12.
DR IntAct; O49485; 1.
DR STRING; 3702.AT4G34200.1; -.
DR SwissPalm; O49485; -.
DR PaxDb; O49485; -.
DR PRIDE; O49485; -.
DR ProMEX; O49485; -.
DR ProteomicsDB; 232974; -.
DR EnsemblPlants; AT4G34200.1; AT4G34200.1; AT4G34200.
DR GeneID; 829568; -.
DR Gramene; AT4G34200.1; AT4G34200.1; AT4G34200.
DR KEGG; ath:AT4G34200; -.
DR Araport; AT4G34200; -.
DR TAIR; locus:2124266; AT4G34200.
DR eggNOG; KOG0068; Eukaryota.
DR HOGENOM; CLU_019796_8_1_1; -.
DR InParanoid; O49485; -.
DR OMA; NIAGMQV; -.
DR OrthoDB; 911009at2759; -.
DR PhylomeDB; O49485; -.
DR BioCyc; ARA:AT4G34200-MON; -.
DR BRENDA; 1.1.1.95; 399.
DR SABIO-RK; O49485; -.
DR UniPathway; UPA00135; UER00196.
DR PRO; PR:O49485; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O49485; baseline and differential.
DR Genevisible; O49485; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; HDA:TAIR.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IMP:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0006564; P:L-serine biosynthetic process; IEA:InterPro.
DR GO; GO:0009561; P:megagametogenesis; IMP:TAIR.
DR GO; GO:0009555; P:pollen development; IMP:TAIR.
DR GO; GO:0000096; P:sulfur amino acid metabolic process; IMP:TAIR.
DR Gene3D; 3.30.1330.90; -; 1.
DR InterPro; IPR045865; ACT-like_dom_sf.
DR InterPro; IPR002912; ACT_dom.
DR InterPro; IPR015878; Ado_hCys_hydrolase_NAD-bd.
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 SMART; SM00997; AdoHcyase_NAD; 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 Chloroplast; NAD; Oxidoreductase; Plastid; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..54
FT /note="Chloroplast"
FT /evidence="ECO:0000305"
FT CHAIN 55..603
FT /note="D-3-phosphoglycerate dehydrogenase 1, chloroplastic"
FT /id="PRO_0000430236"
FT DOMAIN 531..603
FT /note="ACT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01007"
FT ACT_SITE 291
FT /evidence="ECO:0000250"
FT ACT_SITE 320
FT /evidence="ECO:0000250"
FT ACT_SITE 339
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 210..211
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 230
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 289..291
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 315
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 339..342
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT CONFLICT 279
FT /note="K -> N (in Ref. 4; AAM60833)"
FT /evidence="ECO:0000305"
FT CONFLICT 354
FT /note="E -> K (in Ref. 4; AAM60833)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 603 AA; 63325 MW; B53BE9D35A85CADF CRC64;
MSATAAASSS IAVATNSLRN VTLSSRSPLP SAISVAFPSR GRNTLQRRLV LVSCSTGDGS
KPTILVAEKL GDAGIKLLED VANVDCSYNM TPEELNIKIS LCDALIVRSG TKVGREVFES
SHGRLKVVGR AGVGIDNVDL SAATEFGCLV VNAPTANTIA AAEHGIALMA AMARNVAQAD
ASVKAGEWKR NKYVGVSLVG KTLAVLGFGK VGTEVARRAK GLGMRVIAHD PYAPADRAHA
IGVDLVSFDE ALATADFISL HMPLTPTTSK ILNDETFAKM KKGVRIVNVA RGGVIDEDAL
VRALDAGIVA QAALDVFTKE PPAKDSKLVQ HERVTVTPHL GASTMEAQEG VAIEIAEAVV
GALNGELAAT AVNAPMVSAE VLTELKPYVV LAEKLGRLAV QLVAGGSGVK NAKITYASAR
ATDDLDTRLL RAMITKGIIE PISDVYVNLV NADFTAKQRG LRLSEERVLL DGSPESPLET
ITVQLSNVES KFASSLSESG EVKVEGKVKD GVPHLTKVGS FEVDVTLEGS IILCRQVDQP
GMIGTVGSIL GESNVNVNFM SVGRIAPRKQ AIMAIGVDDI PSKETLKKIG EIPAVEEFVF
LKL
