6PGD3_ARATH
ID 6PGD3_ARATH Reviewed; 487 AA.
AC Q9FFR3; Q8LG34;
DT 06-FEB-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=6-phosphogluconate dehydrogenase, decarboxylating 3, chloroplastic {ECO:0000305};
DE EC=1.1.1.44 {ECO:0000250|UniProtKB:Q9FWA3};
GN Name=PGD3 {ECO:0000303|PubMed:26941195};
GN OrderedLocusNames=At5g41670 {ECO:0000312|Araport:AT5G41670};
GN ORFNames=MBK23.20 {ECO:0000312|EMBL:BAB11473.1};
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=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
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 REVIEW.
RX PubMed=12753973; DOI=10.1016/s1369-5266(03)00039-6;
RA Kruger N.J., von Schaewen A.;
RT "The oxidative pentose phosphate pathway: structure and organisation.";
RL Curr. Opin. Plant Biol. 6:236-246(2003).
RN [6]
RP GENE FAMILY.
RX PubMed=17490480; DOI=10.1186/1471-2164-8-116;
RA Settles A.M., Holding D.R., Tan B.C., Latshaw S.P., Liu J., Suzuki M.,
RA Li L., O'Brien B.A., Fajardo D.S., Wroclawska E., Tseung C.W., Lai J.,
RA Hunter C.T. III, Avigne W.T., Baier J., Messing J., Hannah L.C., Koch K.E.,
RA Becraft P.W., Larkins B.A., McCarty D.R.;
RT "Sequence-indexed mutations in maize using the UniformMu transposon-tagging
RT population.";
RL BMC Genomics 8:116-116(2007).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [8]
RP SUBCELLULAR LOCATION.
RX PubMed=26941195; DOI=10.1104/pp.15.01301;
RA Hoelscher C., Lutterbey M.C., Lansing H., Meyer T., Fischer K.,
RA von Schaewen A.;
RT "Defects in peroxisomal 6-phosphogluconate dehydrogenase isoform PGD2
RT prevent gametophytic interaction in Arabidopsis thaliana.";
RL Plant Physiol. 171:192-205(2016).
RN [9]
RP HOMODIMERIZATION, AND HETERODIMERIZATION.
RX PubMed=27366940; DOI=10.1080/15592324.2016.1207034;
RA Lutterbey M.C., von Schaewen A.;
RT "Analysis of homo- and hetero-dimerization among the three 6-
RT phosphogluconate dehydrogenase isoforms of Arabidopsis.";
RL Plant Signal. Behav. 11:E1207034-E1207034(2016).
CC -!- FUNCTION: Catalyzes the oxidative decarboxylation of 6-phosphogluconate
CC to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP
CC to NADPH. {ECO:0000250|UniProtKB:Q9FWA3}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=6-phospho-D-gluconate + NADP(+) = CO2 + D-ribulose 5-phosphate
CC + NADPH; Xref=Rhea:RHEA:10116, ChEBI:CHEBI:16526, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58121, ChEBI:CHEBI:58349, ChEBI:CHEBI:58759; EC=1.1.1.44;
CC Evidence={ECO:0000250|UniProtKB:Q9FWA3};
CC -!- PATHWAY: Carbohydrate degradation; pentose phosphate pathway; D-
CC ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step
CC 3/3. {ECO:0000305}.
CC -!- SUBUNIT: Forms homodimer (PubMed:27366940). Forms heterodimers with
CC PGD1 or PGD2 (PubMed:27366940). {ECO:0000269|PubMed:27366940}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:26941195}. Cytoplasm, cytosol
CC {ECO:0000269|PubMed:26941195}.
CC -!- SIMILARITY: Belongs to the 6-phosphogluconate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; AB005233; BAB11473.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94705.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94706.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM71118.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM71119.1; -; Genomic_DNA.
DR EMBL; AY125503; AAM78095.1; -; mRNA.
DR EMBL; BT002261; AAN72272.1; -; mRNA.
DR EMBL; AY084486; AAM61057.1; -; mRNA.
DR RefSeq; NP_001318724.1; NM_001344409.1.
DR RefSeq; NP_001332670.1; NM_001344410.1.
DR RefSeq; NP_198982.1; NM_123531.3.
DR RefSeq; NP_851113.1; NM_180782.3.
DR AlphaFoldDB; Q9FFR3; -.
DR SMR; Q9FFR3; -.
DR BioGRID; 19420; 17.
DR IntAct; Q9FFR3; 2.
DR STRING; 3702.AT5G41670.2; -.
DR iPTMnet; Q9FFR3; -.
DR SwissPalm; Q9FFR3; -.
DR PaxDb; Q9FFR3; -.
DR PRIDE; Q9FFR3; -.
DR ProMEX; Q9FFR3; -.
DR ProteomicsDB; 244527; -.
DR EnsemblPlants; AT5G41670.1; AT5G41670.1; AT5G41670.
DR EnsemblPlants; AT5G41670.2; AT5G41670.2; AT5G41670.
DR EnsemblPlants; AT5G41670.3; AT5G41670.3; AT5G41670.
DR EnsemblPlants; AT5G41670.4; AT5G41670.4; AT5G41670.
DR GeneID; 834169; -.
DR Gramene; AT5G41670.1; AT5G41670.1; AT5G41670.
DR Gramene; AT5G41670.2; AT5G41670.2; AT5G41670.
DR Gramene; AT5G41670.3; AT5G41670.3; AT5G41670.
DR Gramene; AT5G41670.4; AT5G41670.4; AT5G41670.
DR KEGG; ath:AT5G41670; -.
DR Araport; AT5G41670; -.
DR TAIR; locus:2160422; AT5G41670.
DR eggNOG; KOG2653; Eukaryota.
DR HOGENOM; CLU_024540_4_2_1; -.
DR InParanoid; Q9FFR3; -.
DR OMA; SHGIDKK; -.
DR OrthoDB; 847823at2759; -.
DR PhylomeDB; Q9FFR3; -.
DR BioCyc; ARA:AT5G41670-MON; -.
DR BRENDA; 1.1.1.44; 399.
DR UniPathway; UPA00115; UER00410.
DR PRO; PR:Q9FFR3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FFR3; baseline and differential.
DR Genevisible; Q9FFR3; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0099503; C:secretory vesicle; HDA:TAIR.
DR GO; GO:0050661; F:NADP binding; IBA:GO_Central.
DR GO; GO:0008114; F:phosphogluconate 2-dehydrogenase activity; IDA:TAIR.
DR GO; GO:0004616; F:phosphogluconate dehydrogenase (decarboxylating) activity; IEA:UniProtKB-EC.
DR GO; GO:0046177; P:D-gluconate catabolic process; IBA:GO_Central.
DR GO; GO:0009051; P:pentose-phosphate shunt, oxidative branch; IGI:TAIR.
DR GO; GO:0009750; P:response to fructose; IEP:TAIR.
DR GO; GO:0009749; P:response to glucose; IEP:TAIR.
DR GO; GO:0009744; P:response to sucrose; IEP:TAIR.
DR Gene3D; 1.10.1040.10; -; 1.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013328; 6PGD_dom2.
DR InterPro; IPR006114; 6PGDH_C.
DR InterPro; IPR006113; 6PGDH_Gnd/GntZ.
DR InterPro; IPR006115; 6PGDH_NADP-bd.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR006183; Pgluconate_DH.
DR PANTHER; PTHR11811; PTHR11811; 1.
DR Pfam; PF00393; 6PGD; 1.
DR Pfam; PF03446; NAD_binding_2; 1.
DR PIRSF; PIRSF000109; 6PGD; 1.
DR PRINTS; PR00076; 6PGDHDRGNASE.
DR SMART; SM01350; 6PGD; 1.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR00873; gnd; 1.
PE 1: Evidence at protein level;
KW Acetylation; Chloroplast; Cytoplasm; Gluconate utilization; NADP;
KW Oxidoreductase; Pentose shunt; Plastid; Reference proteome.
FT CHAIN 1..487
FT /note="6-phosphogluconate dehydrogenase, decarboxylating 3,
FT chloroplastic"
FT /id="PRO_0000421099"
FT ACT_SITE 188
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT ACT_SITE 195
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 13..18
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 36..38
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 80..82
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 108
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 108
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 134..136
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 191..192
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 196
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 266
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 293
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 458
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 464
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CONFLICT 40
FT /note="S -> P (in Ref. 4; AAM61057)"
FT /evidence="ECO:0000305"
FT CONFLICT 91
FT /note="S -> T (in Ref. 4; AAM61057)"
FT /evidence="ECO:0000305"
FT CONFLICT 395
FT /note="P -> T (in Ref. 4; AAM61057)"
FT /evidence="ECO:0000305"
FT CONFLICT 454
FT /note="Missing (in Ref. 4; AAM61057)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 487 AA; 53318 MW; ABB2D413CEA15CF2 CRC64;
MESVALSRIG LAGLAVMGQN LALNIADKGF PISVYNRTTS KVDETLDRAS NEGKLPVAGQ
YSPRDFVLSI QRPRSVIILV KAGAPVDQTI SALSEYMEPG DCIIDGGNEW YQNTERRIVE
AEKKGLLYLG MGVSGGEEGA RNGPSLMPGG SFTAYNNVKD ILEKVAAQVE DGPCVTYIGE
GGSGNFVKMV HNGIEYGDMQ LISEAYDVLK NVGGLSNDEL AEIFTEWNRG ELESFLVEIT
SDIFRVKDDY GDGELVDKIL DKTGMKGTGK WTVQQAAELS VAAPTIAASL DCRYLSGLKD
ERENAAKVLE EAGLKEDIGS ASRGVDKKRL IDDVRQALYA SKICSYAQGM NLLRAKSLEK
GWDLNLGEMA RIWKGGCIIR AVFLDRIKKA YQRNPNLASL VVDPDFAKEM VQRQAAWRRV
VGLAISAGIS TPGMCASLAY FDTYRRARLP ANLVQAQRDL FGAHTYERTD RPGAYHTEWT
KLARKSQ
