PPDK2_ORYSJ
ID PPDK2_ORYSJ Reviewed; 887 AA.
AC Q75KR1; Q0DQZ4; Q10J68;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Pyruvate, phosphate dikinase 2;
DE EC=2.7.9.1;
DE AltName: Full=Pyruvate, orthophosphate dikinase 2;
GN Name=PPDK2; Synonyms=CPDK2; OrderedLocusNames=Os03g0432100, LOC_Os03g31750;
GN ORFNames=OsJ_010907, OSJNBa0036E17.10;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
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 [3]
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 [4]
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 [5]
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).
CC -!- FUNCTION: Formation of phosphoenolpyruvate.
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 -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- MISCELLANEOUS: This gene codes only for the short cytoplasmic isoform
CC of PPDK.
CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABF96770.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF12344.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC099041; AAR87148.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF96769.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF96770.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008209; BAF12344.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000140; EAZ27424.1; -; Genomic_DNA.
DR RefSeq; XP_015633061.1; XM_015777575.1.
DR AlphaFoldDB; Q75KR1; -.
DR SMR; Q75KR1; -.
DR STRING; 4530.OS03T0432100-01; -.
DR iPTMnet; Q75KR1; -.
DR PaxDb; Q75KR1; -.
DR PRIDE; Q75KR1; -.
DR GeneID; 4333181; -.
DR KEGG; osa:4333181; -.
DR InParanoid; Q75KR1; -.
DR OrthoDB; 225519at2759; -.
DR BRENDA; 2.7.9.1; 8948.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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: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 3: Inferred from homology;
KW ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Phosphoprotein; Pyruvate; Reference proteome;
KW Transferase.
FT CHAIN 1..887
FT /note="Pyruvate, phosphate dikinase 2"
FT /id="PRO_0000343517"
FT ACT_SITE 469
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 847
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 575
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 632
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 761
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 761
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 782
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 783
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 784
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 785
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 785
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 467
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250"
SQ SEQUENCE 887 AA; 96553 MW; 06174CA51296CA5F CRC64;
MAPAAHRDGA AEAVGQRVFH FGKGRSDGNK TMKDLLGGKG ANLAEMASIG LSVPPGFTVS
TEACQQYQAQ KAMPAGLWDE ILAALTWVEG NMGAVLGDPR RPLLLSVRSG AAVSMPGMMD
TVLNLGLNDH VVAGLAHRSG ERFAYDSYRR FLDMFGNVVM DIPHSLFEEK IEAMKAALGL
RNDTELTARD LKELVAQYKN VYVEAKGEEF PSDPKKQLHL SVLAVFNSWD SARAKKYRSI
NQITGLKGTA VNVQCMVFGN MGDTSGTGVL FTRNPSTGER KLYGEFLVNA QGEDVVAGIR
TPQDLDTMKD CMPEPYAELV ENCKILESHY KEMMDIEFTV QENRLWMLQC RTGKRTGKGA
VKIAVDMVNE GLIDRRSAIK MVEPRHLDQL LHPQFESPSS YGDKVIATGL PASPGAAVGQ
IVFTADDAEA WHAQGKSVIL VRTETSPEDV GGMNAAAGIL TARGGMTSHA AVVARGWGKC
CVAGCSGIRV NDAEKVVLVA DKVLCEGEWL SLNGSTGEVI LGKLPLSPPA LSGDLGEFMS
WVDEVKKLKV KANADTPADA LTARNNGAEG IGLCRTEHMF FSSDERIKAM RQMIMAETIE
HRQIALDRLL PYQRLDFEGI FRAMDGLPVT IRLLDPPLHE FLPEGNVEDM VRLLSSGNVY
TQEEILTRIE KLSEVNPMLG FRGCRLGISY PELTAMQARA IFEAAISMTE QGVKVFPEIM
VPLIGTPQEL AQQVDVIREV AEKVFANAET TISYKIGSMI EVPRAALIAD EIAALAEFFS
FGTNDLTQMT FGYSRDDVGK FLPTYLSKGI LQNDPFEVFD QKGVGELVKV AVERGRKARP
DLEVGICGEH GGEPSSVAFF AKVGLNYVSC SPFRVPIARL AAAQVML
