SERA3_ARATH
ID SERA3_ARATH Reviewed; 588 AA.
AC Q9LT69; Q94B47;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase 3, chloroplastic;
DE EC=1.1.1.95 {ECO:0000269|PubMed:24368794};
DE Flags: Precursor;
GN Name=PGDH3; Synonyms=3-PGDH; OrderedLocusNames=At3g19480;
GN ORFNames=MLD14.22;
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
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] OF 73-588.
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 FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
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 [5]
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). {ECO:0000269|PubMed:24058165,
CC 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 1 mM serine.
CC {ECO:0000269|PubMed:24368794}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.006 mM for 3-phospho-D-glycerate (at pH 8.1)
CC {ECO:0000269|PubMed:24368794};
CC KM=0.239 mM for NAD(+) (at pH 8.1) {ECO:0000269|PubMed:24368794};
CC KM=2.559 mM for 3-phospho-D-glycerate (at pH 7.2)
CC {ECO:0000269|PubMed:24368794};
CC KM=0.551 mM for NAD(+) (at pH 7.2) {ECO:0000269|PubMed:24368794};
CC Vmax=137.6 umol/min/mg enzyme (at pH 8.1)
CC {ECO:0000269|PubMed:24368794};
CC Vmax=93.7 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: Expressed in aerial parts. Not detected in roots
CC and meristematic tissue. Expressed in cotyledons, adult leaves, stigma
CC and anther filaments. Detected in the embryo.
CC {ECO:0000269|PubMed:24058165, ECO:0000269|PubMed:24368794}.
CC -!- INDUCTION: Up-regulated in the aerial parts by dark treatment. Not
CC regulated by high CO(2) levels. {ECO:0000269|PubMed:24058165}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:24058165}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; AB025624; BAB02473.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76246.1; -; Genomic_DNA.
DR EMBL; AY042858; AAK68798.1; -; mRNA.
DR RefSeq; NP_566637.2; NM_112835.4.
DR AlphaFoldDB; Q9LT69; -.
DR SMR; Q9LT69; -.
DR BioGRID; 6815; 11.
DR STRING; 3702.AT3G19480.1; -.
DR iPTMnet; Q9LT69; -.
DR PaxDb; Q9LT69; -.
DR PRIDE; Q9LT69; -.
DR ProMEX; Q9LT69; -.
DR ProteomicsDB; 232955; -.
DR EnsemblPlants; AT3G19480.1; AT3G19480.1; AT3G19480.
DR GeneID; 821482; -.
DR Gramene; AT3G19480.1; AT3G19480.1; AT3G19480.
DR KEGG; ath:AT3G19480; -.
DR Araport; AT3G19480; -.
DR TAIR; locus:2090649; AT3G19480.
DR eggNOG; KOG0068; Eukaryota.
DR HOGENOM; CLU_019796_8_1_1; -.
DR InParanoid; Q9LT69; -.
DR OMA; PAERACA; -.
DR OrthoDB; 911009at2759; -.
DR PhylomeDB; Q9LT69; -.
DR BioCyc; ARA:AT3G19480-MON; -.
DR BRENDA; 1.1.1.95; 399.
DR SABIO-RK; Q9LT69; -.
DR UniPathway; UPA00135; UER00196.
DR PRO; PR:Q9LT69; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LT69; baseline and differential.
DR Genevisible; Q9LT69; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0003954; F:NADH dehydrogenase activity; IDA:TAIR.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0006564; P:L-serine biosynthetic process; IEA:InterPro.
DR GO; GO:0009643; P:photosynthetic acclimation; 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..38
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 39..588
FT /note="D-3-phosphoglycerate dehydrogenase 3, chloroplastic"
FT /id="PRO_0000430237"
FT DOMAIN 516..588
FT /note="ACT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01007"
FT ACT_SITE 276
FT /evidence="ECO:0000250"
FT ACT_SITE 305
FT /evidence="ECO:0000250"
FT ACT_SITE 324
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 195..196
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 215
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 274..276
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 300
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 324..327
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
SQ SEQUENCE 588 AA; 62122 MW; E4C9A35BE86D3AD5 CRC64;
MATSLNLSSI FSSSSRLVTT PSSVFPIRQR RRIILVTSSS SGGGGKPTIL VTEKLGQAGI
DLLKKYANVD CSYDLSLEEL CTKISLCDAL IVRSGTKVGR DVFESSRGRL KVVGRAGVGI
DNVDLAAATE YGCLVVNAPT ANTVAAAEHG IALLTAMARN IAQADASIKA GKWTRNKYVG
VSLVGKTLAV LGFGKVGSEV ARRARGLGMH VITHDPYAPA DRARAIGVEL VSFEVAISTA
DFISLHLPLT AATSKMMNDV TFAMMKKGVR IVNVARGGVI DEEALLRALD SGIVAQAALD
VFTVEPPVKD NKLVLHESVT ATPHLGASTM EAQEGVSIEV AEAVIGALRG ELAATAVNAP
MVPLEVLREL KPYVVLAEKL GRLAVQLVTG GSGVNAVKVT YASSRAPDDL DTRLLRAMVI
KGIIEPISSV FINLVNSDYI AKQRGVKISE ERMVLDGSPE NPIEYITVRI ANVESRFASA
LSESGEIKVE GRVKQGVPSL TKVGLFGVDV SLEGSVILCR QVDQPGMIGK VASILGDENV
NVSFMSVGRI APGKQAVMAI GVDEQPSKET LKKIGDIPAI EEFVFLKL
