PPDK_FLATR
ID PPDK_FLATR Reviewed; 953 AA.
AC P22221; Q42738; Q42739;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Pyruvate, phosphate dikinase, chloroplastic;
DE EC=2.7.9.1 {ECO:0000250|UniProtKB:P11155};
DE AltName: Full=Pyruvate, orthophosphate dikinase;
DE Flags: Precursor;
GN Name=PPDK; Synonyms=PDK;
OS Flaveria trinervia (Clustered yellowtops) (Oedera trinervia).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; campanulids; Asterales; Asteraceae; Asteroideae;
OC Heliantheae alliance; Tageteae; Flaveria.
OX NCBI_TaxID=4227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Leaf;
RX PubMed=2172023; DOI=10.1016/0014-5793(90)81064-u;
RA Rosche E., Westhoff P.;
RT "Primary structure of pyruvate, orthophosphate dikinase in the
RT dicotyledonous C4 plant Flaveria trinervia.";
RL FEBS Lett. 273:116-121(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, AND INDUCTION.
RC TISSUE=Leaf;
RX PubMed=8541493; DOI=10.1007/bf00041157;
RA Rosche E., Westhoff P.;
RT "Genomic structure and expression of the pyruvate, orthophosphate dikinase
RT gene of the dicotyledonous C4 plant Flaveria trinervia (Asteraceae).";
RL Plant Mol. Biol. 29:663-678(1995).
CC -!- FUNCTION: Formation of phosphoenolpyruvate, which is the primary
CC acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.
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 (By similarity). {ECO:0000250}.
CC -!- PATHWAY: Photosynthesis; C4 acid pathway.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:8541493}. Cytoplasm {ECO:0000269|PubMed:8541493}.
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=P22221-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P22221-4; Sequence=VSP_034607, VSP_034608;
CC -!- TISSUE SPECIFICITY: Isoform 1 mainly localized in mesophyll cells and
CC only a low level is found in bundle sheath cells. Isoform 2 is
CC expressed in roots and stems. {ECO:0000269|PubMed:8541493}.
CC -!- INDUCTION: [Isoform 1]: Light-inducible. {ECO:0000269|PubMed:8541493}.
CC -!- INDUCTION: [Isoform 2]: Dark-inducible. {ECO:0000269|PubMed:8541493}.
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. {ECO:0000250}.
CC -!- PTM: Phosphorylation of Thr-533 in the dark inactivates the enzyme.
CC Dephosphorylation upon light stimulation reactivates the enzyme (By
CC similarity). {ECO:0000250}.
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: [Isoform 2]: Produced by alternative promoter usage.
CC Cytoplasmic. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA55702.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAA55703.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; X57141; CAA40420.1; -; mRNA.
DR EMBL; X79095; CAA55702.1; ALT_SEQ; Genomic_DNA.
DR EMBL; X79095; CAA55703.1; ALT_SEQ; Genomic_DNA.
DR PIR; S12894; S12894.
DR PIR; S61410; S61410.
DR PDB; 5JVJ; X-ray; 2.90 A; A/B=80-953.
DR PDB; 5JVL; X-ray; 2.90 A; A/B/C/D=80-953.
DR PDB; 5LU4; X-ray; 2.90 A; A/B=80-953.
DR PDBsum; 5JVJ; -.
DR PDBsum; 5JVL; -.
DR PDBsum; 5LU4; -.
DR AlphaFoldDB; P22221; -.
DR SMR; P22221; -.
DR BRENDA; 2.7.9.1; 2270.
DR UniPathway; UPA00322; -.
DR GO; GO:0009507; C:chloroplast; 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: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; 2.
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 3D-structure; Alternative promoter usage; ATP-binding; Chloroplast;
KW Cytoplasm; Kinase; Magnesium; Metal-binding; Nucleotide-binding;
KW Phosphoprotein; Photosynthesis; Plastid; Pyruvate; Transferase;
KW Transit peptide.
FT TRANSIT 1..77
FT /note="Chloroplast"
FT /evidence="ECO:0000250"
FT CHAIN 78..953
FT /note="Pyruvate, phosphate dikinase, chloroplastic"
FT /id="PRO_0000023562"
FT REGION 55..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 535
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 913
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 641
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 698
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 827
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 827
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 848
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 849
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 850
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 851
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 851
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 533
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..79
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_034607"
FT VAR_SEQ 80..81
FT /note="KK -> MQ (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_034608"
FT CONFLICT 143
FT /note="L -> S (in Ref. 1; CAA40420)"
FT /evidence="ECO:0000305"
FT STRAND 82..87
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 90..93
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 98..100
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 103..113
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 126..134
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 143..158
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:5JVL"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:5JVL"
FT STRAND 171..176
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 195..205
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 207..224
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 230..242
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:5JVL"
FT HELIX 254..272
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 280..295
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 300..307
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 316..321
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 332..339
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 341..343
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 349..355
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 358..363
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 371..377
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 379..396
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 400..407
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 410..418
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 423..435
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 441..447
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 450..455
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 460..462
FT /evidence="ECO:0007829|PDB:5JVL"
FT HELIX 464..470
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 471..474
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 476..479
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 481..488
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 491..500
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 504..509
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 513..515
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 516..521
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 522..529
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 535..542
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 546..549
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 555..557
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 558..561
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 562..565
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 568..571
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 575..579
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 580..582
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 584..588
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 599..611
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 614..619
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 623..631
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 636..641
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 642..644
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 650..660
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 665..689
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 690..692
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 693..698
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 704..707
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 713..724
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 728..738
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 743..745
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 750..755
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 757..775
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 776..778
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 782..787
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 793..814
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 821..826
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 829..833
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 835..839
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 843..847
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 849..857
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 861..864
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 865..873
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 881..883
FT /evidence="ECO:0007829|PDB:5JVJ"
FT TURN 887..889
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 890..904
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 909..912
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 915..918
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 920..929
FT /evidence="ECO:0007829|PDB:5JVJ"
FT STRAND 932..936
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 938..940
FT /evidence="ECO:0007829|PDB:5JVJ"
FT HELIX 941..950
FT /evidence="ECO:0007829|PDB:5JVJ"
SQ SEQUENCE 953 AA; 103975 MW; 9C13CA6C06A8F7C6 CRC64;
MMSSLSVEGM LLKSARESCL PARVNQRRNG DLRRLNHHRQ SSFVRCLTPA RVSRPELRSS
GLTPPRAVLN PVSPPVTTAK KRVFTFGKGR SEGNRDMKSL LGGKGANLAE MSSIGLSVPP
GLTISTEACE EYQQNGKSLP PGLWDEISEG LDYVQKEMSA SLGDPSKPLL LSVRSGAAIS
MPGMMDTVLN LGLNDEVVAG LAGKSGARFA YDSYRRFLDM FGNVVMGIPH SLFDEKLEQM
KAEKGIHLDT DLTAADLKDL VEKYKNVYVE AKGEKFPTDP KKQLELAVNA VFDSWDSPRA
NKYRSINQIT GLKGTAVNIQ SMVFGNMGNT SGTGVLFTRN PSTGEKKLYG EFLINAQGED
VVAGIRTPED LGTMETCMPE AYKELVENCE ILERHYKDMM DIEFTVQENR LWMLQCRTGK
RTGKGAVRIA VDMVNEGLID TRTAIKRVET QHLDQLLHPQ FEDPSAYKSH VVATGLPASP
GAAVGQVCFS AEDAETWHAQ GKSAILVRTE TSPEDVGGMH AAAGILTARG GMTSHAAVVA
RGWGKCCVSG CADIRVNDDM KIFTIGDRVI KEGDWLSLNG TTGEVILGKQ LLAPPAMSND
LEIFMSWADQ ARRLKVMANA DTPNDALTAR NNGAQGIGLC RTEHMFFASD ERIKAVRKMI
MAVTPEQRKV ALDLLLPYQR SDFEGIFRAM DGLPVTIRLL DPPLHEFLPE GDLEHIVNEL
AVDTGMSADE IYSKIENLSE VNPMLGFRGC RLGISYPELT EMQVRAIFQA AVSMTNQGVT
VIPEIMVPLV GTPQELRHQI SVIRGVAANV FAEMGVTLEY KVGTMIEIPR AALIAEEIGK
EADFFSFGTN DLTQMTFGYS RDDVGKFLQI YLAQGILQHD PFEVIDQKGV GQLIKMATEK
GRAANPSLKV GICGEHGGEP SSVAFFDGVG LDYVSCSPFR VPIARLAAAQ VIV
