PPDK1_ORYSJ
ID PPDK1_ORYSJ Reviewed; 947 AA.
AC Q6AVA8; A3B3X0; B7EEB8; O24612; Q7DN52;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2004, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Pyruvate, phosphate dikinase 1, chloroplastic;
DE EC=2.7.9.1;
DE AltName: Full=OsPPDKB;
DE AltName: Full=Pyruvate, orthophosphate dikinase 1;
DE Flags: Precursor;
GN Name=PPDK1; Synonyms=CPDK1, PPDKB;
GN OrderedLocusNames=Os05g0405000, LOC_Os05g33570;
GN ORFNames=OJ1174_H11.5, OsJ_017742;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS 1 AND 2), ALTERNATIVE
RP PROMOTER USAGE, FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION,
RP DEVELOPMENTAL STAGE, AND INDUCTION.
RC STRAIN=cv. Nipponbare;
RX PubMed=9278162; DOI=10.1023/a:1005884515840;
RA Imaizumi N., Ku M.S.B., Ishihara K., Samejima M., Kaneko S., Matsuoka M.;
RT "Characterization of the gene for pyruvate,orthophosphate dikinase from
RT rice, a C3 plant, and a comparison of structure and expression between C3
RT and C4 genes for this protein.";
RL Plant Mol. Biol. 34:701-716(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP PHOSPHORYLATION, AND ACTIVITY REGULATION.
RX PubMed=11950985; DOI=10.1104/pp.010806;
RA Chastain C.J., Fries J.P., Vogel J.A., Randklev C.L., Vossen A.P.,
RA Dittmer S.K., Watkins E.E., Fiedler L.J., Wacker S.A., Meinhover K.C.,
RA Sarath G., Chollet R.;
RT "Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants
RT undergoes light-/dark-induced reversible phosphorylation.";
RL Plant Physiol. 128:1368-1378(2002).
RN [9]
RP FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=15941402; DOI=10.1111/j.1365-313x.2005.02423.x;
RA Kang H.-G., Park S., Matsuoka M., An G.;
RT "White-core endosperm floury endosperm-4 in rice is generated by knockout
RT mutations in the C-type pyruvate orthophosphate dikinase gene (OsPPDKB).";
RL Plant J. 42:901-911(2005).
RN [10]
RP FUNCTION, TISSUE SPECIFICITY, PHOSPHORYLATION, AND DEVELOPMENTAL STAGE.
RX PubMed=16596412; DOI=10.1007/s00425-006-0259-3;
RA Chastain C.J., Heck J.W., Colquhoun T.A., Voge D.G., Gu X.-Y.;
RT "Posttranslational regulation of pyruvate, orthophosphate dikinase in
RT developing rice (Oryza sativa) seeds.";
RL Planta 224:924-934(2006).
CC -!- FUNCTION: Formation of phosphoenolpyruvate. The cytoplasmic isoform
CC supports the biosynthetic processes in the nascent endosperm and
CC provides an efficient mechanism for glycolytic ATP synthesis in oxygen
CC depleted tissues. May be involved in regulating the flux of carbon into
CC starch and fatty acids of seeds and in the remobilization of nitrogen
CC reserves in senescing leaves. {ECO:0000269|PubMed:15941402,
CC ECO:0000269|PubMed:16596412, ECO:0000269|PubMed:9278162}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + phosphate + pyruvate = AMP + diphosphate + H(+) +
CC phosphoenolpyruvate; Xref=Rhea:RHEA:10756, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58702, ChEBI:CHEBI:456215; EC=2.7.9.1;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P11155};
CC -!- ACTIVITY REGULATION: Activated by light-induced dephosphorylation.
CC Inhibited by dark-induced phosphorylation. Both reactions are catalyzed
CC by PDRP1. {ECO:0000269|PubMed:11950985}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:9278162}. Cytoplasm {ECO:0000269|PubMed:9278162}.
CC Note=Isoform 1 is targeted to the chloroplast while isoform 2 is found
CC in the cytoplasm.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative promoter usage; Named isoforms=2;
CC Name=1;
CC IsoId=Q6AVA8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6AVA8-2; Sequence=VSP_034611, VSP_034612;
CC -!- TISSUE SPECIFICITY: Isoform 1 is only expressed in green leaves.
CC Isoform 2 is found in roots, stems, rachis branches, leaf sheaths,
CC green leaves and spikelets. The non-phosphorylated PPDK in mature seeds
CC is endosperm-localized. {ECO:0000269|PubMed:16596412,
CC ECO:0000269|PubMed:9278162}.
CC -!- DEVELOPMENTAL STAGE: Massively expressed in 10 days post-pollination
CC seeds and then shows a steep decline as seed maturation proceeds.
CC {ECO:0000269|PubMed:15941402, ECO:0000269|PubMed:16596412,
CC ECO:0000269|PubMed:9278162}.
CC -!- INDUCTION: By light. {ECO:0000269|PubMed:9278162}.
CC -!- DOMAIN: The N-terminal domain contains the ATP/Pi binding site, the
CC central domain the pyrophosphate/phosphate carrier histidine, and the
CC C-terminal domain the pyruvate binding site.
CC -!- PTM: Phosphorylation of Thr-527 in the dark inactivates the enzyme.
CC Dephosphorylation upon light stimulation reactivates the enzyme.
CC Phosphorylation increases during the first 20 days post-pollination and
CC then remains constant through the 40-day mature seed stage.
CC Reactivation by dephosphorylation during germination is negligible.
CC {ECO:0000269|PubMed:11950985, ECO:0000269|PubMed:16596412}.
CC -!- DISRUPTION PHENOTYPE: Plants have a floury-white endosperm.
CC {ECO:0000269|PubMed:15941402}.
CC -!- MISCELLANEOUS: The reaction takes place in three steps, mediated by a
CC phosphocarrier histidine residue located on the surface of the central
CC domain. The two first partial reactions are catalyzed at an active site
CC located on the N-terminal domain, and the third partial reaction is
CC catalyzed at an active site located on the C-terminal domain. For
CC catalytic turnover, the central domain swivels from the concave surface
CC of the N-terminal domain to that of the C-terminal domain (By
CC similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: A second gene codes only for the short cytoplasmic
CC isoform of PPDK.
CC -!- MISCELLANEOUS: [Isoform 2]: Produced by alternative promoter usage.
CC Cytoplasmic. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; D87745; BAA22419.1; -; mRNA.
DR EMBL; D87952; BAA22420.1; -; Genomic_DNA.
DR EMBL; AC104708; AAT85082.1; -; Genomic_DNA.
DR EMBL; AP008211; BAF17421.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS93945.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS93946.1; -; Genomic_DNA.
DR EMBL; CM000142; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK068025; BAG90715.1; -; mRNA.
DR EMBL; AK101783; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; T02979; T02979.
DR RefSeq; XP_015639324.1; XM_015783838.1. [Q6AVA8-1]
DR AlphaFoldDB; Q6AVA8; -.
DR SMR; Q6AVA8; -.
DR IntAct; Q6AVA8; 1.
DR STRING; 4530.OS05T0405000-01; -.
DR PaxDb; Q6AVA8; -.
DR PRIDE; Q6AVA8; -.
DR EnsemblPlants; Os05t0405000-01; Os05t0405000-01; Os05g0405000. [Q6AVA8-1]
DR EnsemblPlants; Os05t0405000-02; Os05t0405000-02; Os05g0405000. [Q6AVA8-2]
DR GeneID; 4338750; -.
DR Gramene; Os05t0405000-01; Os05t0405000-01; Os05g0405000. [Q6AVA8-1]
DR Gramene; Os05t0405000-02; Os05t0405000-02; Os05g0405000. [Q6AVA8-2]
DR KEGG; osa:4338750; -.
DR eggNOG; ENOG502QREJ; Eukaryota.
DR InParanoid; Q6AVA8; -.
DR OMA; RRFVQMY; -.
DR OrthoDB; 225519at2759; -.
DR BRENDA; 2.7.9.1; 8948.
DR Proteomes; UP000000763; Chromosome 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR Genevisible; Q6AVA8; OS.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; IEA:EnsemblPlants.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050242; F:pyruvate, phosphate dikinase activity; IEA:UniProtKB-EC.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0015979; P:photosynthesis; IEA:UniProtKB-KW.
DR GO; GO:0006090; P:pyruvate metabolic process; IEA:InterPro.
DR Gene3D; 3.20.20.60; -; 1.
DR Gene3D; 3.30.1490.20; -; 1.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR008279; PEP-util_enz_mobile_dom.
DR InterPro; IPR018274; PEP_util_AS.
DR InterPro; IPR000121; PEP_util_C.
DR InterPro; IPR023151; PEP_util_CS.
DR InterPro; IPR036637; Phosphohistidine_dom_sf.
DR InterPro; IPR002192; PPDK_AMP/ATP-bd.
DR InterPro; IPR010121; Pyruvate_phosphate_dikinase.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR PANTHER; PTHR22931; PTHR22931; 1.
DR Pfam; PF00391; PEP-utilizers; 1.
DR Pfam; PF02896; PEP-utilizers_C; 1.
DR Pfam; PF01326; PPDK_N; 3.
DR PIRSF; PIRSF000853; PPDK; 1.
DR SUPFAM; SSF51621; SSF51621; 1.
DR SUPFAM; SSF52009; SSF52009; 1.
DR TIGRFAMs; TIGR01828; pyru_phos_dikin; 1.
DR PROSITE; PS00742; PEP_ENZYMES_2; 1.
DR PROSITE; PS00370; PEP_ENZYMES_PHOS_SITE; 1.
PE 1: Evidence at protein level;
KW Alternative promoter usage; ATP-binding; Chloroplast; Cytoplasm; Kinase;
KW Magnesium; Metal-binding; Nucleotide-binding; Phosphoprotein;
KW Photosynthesis; Plastid; Pyruvate; Reference proteome; Transferase;
KW Transit peptide.
FT TRANSIT 1..71
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 72..947
FT /note="Pyruvate, phosphate dikinase 1, chloroplastic"
FT /id="PRO_5000140166"
FT REGION 39..60
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 529
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 907
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 635
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 692
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 821
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 821
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 842
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 843
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 844
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 845
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 845
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 527
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT VAR_SEQ 1..65
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764,
FT ECO:0000303|PubMed:9278162"
FT /id="VSP_034611"
FT VAR_SEQ 66..75
FT /note="VAAPIPTTKK -> MAPAQCARVQ (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764,
FT ECO:0000303|PubMed:9278162"
FT /id="VSP_034612"
FT CONFLICT 425
FT /note="V -> L (in Ref. 1; BAA22420/BAA22419)"
FT /evidence="ECO:0000305"
FT CONFLICT 740
FT /note="G -> D (in Ref. 7; AK101783)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 947 AA; 102788 MW; BF06F0E37FF2079D CRC64;
MPSVSRAVCV QRASGNNGRR CRDGAAAAGR RSVVAQRARH GKPEVAIRSG SGGSARGGHC
SPLRAVAAPI PTTKKRVFHF GKGKSEGNKA MKDLLGGKGA NLAEMASIGL SVPPGFTVST
EACQQYQAAG KTLPAGLWEE IVEGLQWVEE YMAARLGDPA RPLLLSVRSG AAVSMPGMMD
TVLNLGLNDE VAAGLAAKSG DRFAYDSYRR FLDMFGNVVM DIPHALFEEK LEAMKAVKGL
HNDTDLTATD LKELVAQYKD VYVEAKGEPF PSDPKKQLQL AVLAVFNSWD SPRAIKYRSI
NKITGLKGTA VNVQTMVFGN MGNTSGTGVL FTRNPSTGEK KLYGEFLVNA QGEDVVAGIR
TPEDLDAMRD HMPEPYEELV ENCKILESHY KEMMDIEFTV QENRLWMLQC RTGKRTGKGA
VKIAVDMVNE GLVERRTALK MVEPGHLDQL LHPQFENPSG YKDKVIATGL PASPGAAVGQ
IVFTAEDAEA WHAQGKDVIL VRTETSPEDV GGMHAAVGIL TARGGMTSHA AVVARGWGKC
CVSGCSSVRV NDASKIVVIE DKALHEGEWL SLNGSTGEVI IGKQPLCPPA LSGDLETFMS
WVDEVRKLKV MANADTPEDA TTARQNGAEG IGLCRTEHMF FASDERIKAV RQMIMASSLE
LRQKALDRLL PYQRSDFEGI FRAMDGLPVT IRLLDPPLHE FLPEGHVEDM VRELCSETGA
AQDDVLARVE KLSEVNPMLG FRGCRLGISY PELTEMQARA IFEAAITMTN QGIQVFPEIM
VPLVGTPQEL GHQVDVIRQI ANKVFTDMGK TIGYKVGTMI EIPRAALVAD EIAEQAEFFS
FGTNDLTQMT FGYSRDDVGK FLPIYLSQGI LQHDPFEVLD QRGVGELVKL ATERGRKARP
NLKVGICGEH GGEPLSVAFF AKAGLDYVSC SPFRVPIARL AAAQVLL
