GenomeNet

Database: UniProt
Entry: O49485
LinkDB: O49485
Original site: O49485 
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   16-JAN-2019, entry version 146.
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;
GN   ORFNames=F10M10.7;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   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.,
RA   Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
RA   Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
RA   Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
RA   Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
RA   Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
RA   Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
RA   Langham S.-A., McCullagh B., Bilham L., Robben J.,
RA   van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
RA   Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
RA   Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA   Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
RA   Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
RA   Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
RA   De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
RA   van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
RA   Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
RA   Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
RA   Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
RA   Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
RA   Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
RA   Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA   Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
RA   Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
RA   Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
RA   Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
RA   Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
RA   Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
RA   Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
RA   Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
RA   Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
RA   Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
RA   Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
RA   Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
RA   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.,
RA   Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
RA   Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
RA   Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
RA   Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
RA   Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
RA   Chen E., Marra M.A., Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis
RT   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
RT   reference 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.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., 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
RT   of ubiquitinated proteins in plants.";
RL   Mol. Cell. Proteomics 6:601-610(2007).
RN   [6]
RP   FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP   SUBCELLULAR LOCATION, ACTIVITY REGULATION, TISSUE SPECIFICITY,
RP   DISRUPTION PHENOTYPE, 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
RT   pathway is essential for development and required for ammonium
RT   assimilation and 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
CC       serine biosynthesis (PPSB). Required for mature pollen
CC       development. {ECO:0000269|PubMed:24058165,
CC       ECO:0000269|PubMed:24368794}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=3-phospho-D-glycerate + NAD(+) = 3-phosphooxypyruvate +
CC         H(+) + NADH; Xref=Rhea:RHEA:12641, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:18110, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC         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)
CC         {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
CC       from 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
CC       at 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,
CC       high 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}.
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   UniGene; At.21335; -.
DR   UniGene; At.74573; -.
DR   ProteinModelPortal; O49485; -.
DR   SMR; O49485; -.
DR   BioGrid; 14850; 1.
DR   IntAct; O49485; 1.
DR   STRING; 3702.AT4G34200.1; -.
DR   SwissPalm; O49485; -.
DR   PaxDb; O49485; -.
DR   PRIDE; O49485; -.
DR   ProMEX; O49485; -.
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   eggNOG; COG0111; LUCA.
DR   HOGENOM; HOG000136693; -.
DR   InParanoid; O49485; -.
DR   KO; K00058; -.
DR   OMA; NIAGMQV; -.
DR   OrthoDB; 911009at2759; -.
DR   PhylomeDB; O49485; -.
DR   BioCyc; ARA:AT4G34200-MONOMER; -.
DR   Reactome; R-ATH-977347; Serine biosynthesis.
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; IDA:TAIR.
DR   GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
DR   GO; GO:0016020; C:membrane; IDA:TAIR.
DR   GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR   GO; GO:0009536; C:plastid; IDA:TAIR.
DR   GO; GO:0005524; F:ATP binding; IDA:TAIR.
DR   GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR   GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IBA:GO_Central.
DR   GO; GO:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
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   Gene3D; 3.30.1330.90; -; 1.
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   Pfam; PF00389; 2-Hacid_dh; 1.
DR   Pfam; PF02826; 2-Hacid_dh_C; 1.
DR   Pfam; PF01842; ACT; 1.
DR   SMART; SM00997; AdoHcyase_NAD; 1.
DR   SUPFAM; SSF143548; SSF143548; 1.
DR   SUPFAM; SSF51735; SSF51735; 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; Complete proteome; NAD; Oxidoreductase; Plastid;
KW   Reference proteome; Transit peptide.
FT   TRANSIT       1     54       Chloroplast. {ECO:0000305}.
FT   CHAIN        55    603       D-3-phosphoglycerate dehydrogenase 1,
FT                                chloroplastic.
FT                                /FTId=PRO_0000430236.
FT   DOMAIN      531    603       ACT. {ECO:0000255|PROSITE-
FT                                ProRule:PRU01007}.
FT   NP_BIND     210    211       NAD. {ECO:0000250|UniProtKB:P0A9T0}.
FT   NP_BIND     289    291       NAD. {ECO:0000250|UniProtKB:P0A9T0}.
FT   NP_BIND     339    342       NAD. {ECO:0000250|UniProtKB:P0A9T0}.
FT   COMPBIAS    153    185       Ala-rich.
FT   ACT_SITE    291    291       {ECO:0000250}.
FT   ACT_SITE    320    320       {ECO:0000250}.
FT   ACT_SITE    339    339       Proton donor. {ECO:0000250}.
FT   BINDING     230    230       NAD. {ECO:0000250|UniProtKB:P0A9T0}.
FT   BINDING     315    315       NAD. {ECO:0000250|UniProtKB:P0A9T0}.
FT   CONFLICT    279    279       K -> N (in Ref. 4; AAM60833).
FT                                {ECO:0000305}.
FT   CONFLICT    354    354       E -> K (in Ref. 4; AAM60833).
FT                                {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
//
DBGET integrated database retrieval system