6PGD2_ARATH
ID 6PGD2_ARATH Reviewed; 486 AA.
AC Q9FWA3;
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 2 {ECO:0000305};
DE EC=1.1.1.44 {ECO:0000269|PubMed:26941195};
GN Name=PGD2 {ECO:0000303|PubMed:26941195};
GN OrderedLocusNames=At3g02360 {ECO:0000312|Araport:AT3G02360};
GN ORFNames=F11A12.5 {ECO:0000312|EMBL:AAG12595.1};
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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].
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].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
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 [7]
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 [8]
RP FUNCTION, CATALYTIC ACTIVITY, HOMODIMERIZATION, SUBCELLULAR LOCATION, AND
RP DISRUPTION PHENOTYPE.
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 (PubMed:26941195). Required for guided growth of the male
CC gametophytes and interaction between the pollen tube and the ovule
CC (PubMed:26941195). {ECO:0000269|PubMed:26941195}.
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:0000269|PubMed:26941195};
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:26941195, PubMed:27366940). Forms
CC heterodimers with PGD1 or PGD3 (PubMed:27366940).
CC {ECO:0000269|PubMed:26941195, ECO:0000269|PubMed:27366940}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:26941195}.
CC Peroxisome {ECO:0000269|PubMed:26941195}.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality when homozygous
CC (PubMed:26941195). Defects in pollen tube growth (PubMed:26941195).
CC {ECO:0000269|PubMed:26941195}.
CC -!- SIMILARITY: Belongs to the 6-phosphogluconate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; AC068900; AAG12595.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73796.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73797.1; -; Genomic_DNA.
DR EMBL; AF424591; AAL11585.1; -; mRNA.
DR EMBL; BT002299; AAN73296.1; -; mRNA.
DR EMBL; AK227160; BAE99202.1; -; mRNA.
DR EMBL; AY087341; AAM64891.1; -; mRNA.
DR RefSeq; NP_186885.1; NM_111103.6.
DR RefSeq; NP_850502.1; NM_180171.2.
DR AlphaFoldDB; Q9FWA3; -.
DR SMR; Q9FWA3; -.
DR BioGRID; 6496; 20.
DR IntAct; Q9FWA3; 1.
DR STRING; 3702.AT3G02360.2; -.
DR iPTMnet; Q9FWA3; -.
DR PaxDb; Q9FWA3; -.
DR PRIDE; Q9FWA3; -.
DR ProteomicsDB; 245077; -.
DR EnsemblPlants; AT3G02360.1; AT3G02360.1; AT3G02360.
DR EnsemblPlants; AT3G02360.2; AT3G02360.2; AT3G02360.
DR GeneID; 821163; -.
DR Gramene; AT3G02360.1; AT3G02360.1; AT3G02360.
DR Gramene; AT3G02360.2; AT3G02360.2; AT3G02360.
DR KEGG; ath:AT3G02360; -.
DR Araport; AT3G02360; -.
DR TAIR; locus:2074577; AT3G02360.
DR eggNOG; KOG2653; Eukaryota.
DR HOGENOM; CLU_024540_4_2_1; -.
DR InParanoid; Q9FWA3; -.
DR OMA; VIMVKAG; -.
DR OrthoDB; 847823at2759; -.
DR PhylomeDB; Q9FWA3; -.
DR BRENDA; 1.1.1.44; 399.
DR UniPathway; UPA00115; UER00410.
DR PRO; PR:Q9FWA3; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9FWA3; baseline and differential.
DR Genevisible; Q9FWA3; AT.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005777; C:peroxisome; IDA:TAIR.
DR GO; GO:0099503; C:secretory vesicle; HDA:TAIR.
DR GO; GO:0050661; F:NADP binding; IBA:GO_Central.
DR GO; GO:0004616; F:phosphogluconate dehydrogenase (decarboxylating) activity; IDA:TAIR.
DR GO; GO:0046177; P:D-gluconate catabolic process; IBA:GO_Central.
DR GO; GO:0080173; P:male-female gamete recognition during double fertilization forming a zygote and endosperm; IMP:TAIR.
DR GO; GO:0009051; P:pentose-phosphate shunt, oxidative branch; IBA:GO_Central.
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 Cytoplasm; Gluconate utilization; NADP; Oxidoreductase; Pentose shunt;
KW Peroxisome; Reference proteome.
FT CHAIN 1..486
FT /note="6-phosphogluconate dehydrogenase, decarboxylating 2"
FT /id="PRO_0000421100"
FT MOTIF 484..486
FT /note="Microbody targeting signal"
FT /evidence="ECO:0000305|PubMed:26941195"
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 12..17
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 35..37
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 79..81
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 107
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 107
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 133..135
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 456
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P96789"
FT BINDING 462
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P96789"
SQ SEQUENCE 486 AA; 53577 MW; 894395559DAEB020 CRC64;
MAVQPTRIGL AGLAVMGQNL ALNIAEKGFP ISVYNRTTSK VDETVERAKK EGNLPLYGFH
DPESFVKSIQ KPRVIIMLVK AGSPVDQTIK TLSAYLEKGD CIVDGGNEWY ENTERREKAV
AENGFLYLGM GVSGGEEGAR NGPSMMPGGS YEAYKNIEDI VLKVAAQVRD SGPCVTYIGK
GGSGNFVKMV HNGIEYGDMQ LIAEAYDVLK SVGKLSNEEL HSVFSDWNKG ELESFLVEIT
ADIFGIKDDK GDGHLVDKVL DKTGMKGTGK WTVQQAAELS VPAPTIESSL DARFLSGLKD
ERVQAAKVFK AGGFGDILTD QKVDKKQLVD DVRKALYASK ICSYAQGMNL IRAKSIEKGW
GLKLGELARI WKGGCIIRAI FLDRIKQAYD RNAELANLLV DPEFAKEIIE RQSAWRRVVC
LAINSGISTP GMSASLAYFD SYRRERLPAN LVQAQRDYFG AHTYERTDVE GSFHTEWFKI
ARQSKI
