PPDK_FLABR
ID PPDK_FLABR Reviewed; 955 AA.
AC Q39734; Q6LBF3;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Pyruvate, phosphate dikinase, chloroplastic;
DE EC=2.7.9.1 {ECO:0000250|UniProtKB:P11155};
DE AltName: Full=Cold-sensitive pyruvate, orthophosphate dikinase;
DE AltName: Full=Pyruvate, orthophosphate dikinase;
DE Flags: Precursor;
GN Name=PPDK; Synonyms=PDK;
OS Flaveria brownii (Brown's yellowtops).
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=33111;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC TISSUE=Leaf;
RX PubMed=7948930; DOI=10.1007/bf00013761;
RA Rosche E., Streubel M., Westhoff P.;
RT "Primary structure of the photosynthetic pyruvate orthophosphate dikinase
RT of the C3 plant Flaveria pringlei and expression analysis of pyruvate
RT orthophosphate dikinase sequences in C3, C3-C4 and C4 Flaveria species.";
RL Plant Mol. Biol. 26:763-769(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND PROTEIN SEQUENCE OF 72-79.
RC TISSUE=Leaf;
RX PubMed=7766886; DOI=10.1007/bf00037024;
RA Usami S., Ohta S., Komari T., Burnell J.N.;
RT "Cold stability of pyruvate, orthophosphate dikinase of Flaveria brownii.";
RL Plant Mol. Biol. 27:969-980(1995).
RN [3]
RP BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY REGULATION.
RX PubMed=9038349; DOI=10.1016/s0014-5793(97)00015-x;
RA Ohta S., Usami S., Ueki J., Kumashiro T., Komari T., Burnell J.N.;
RT "Identification of the amino acid residues responsible for cold tolerance
RT in Flaveria brownii pyruvate,orthophosphate dikinase.";
RL FEBS Lett. 403:5-9(1997).
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). Very cold-tolerant. {ECO:0000250,
CC ECO:0000269|PubMed:9038349}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=67 uM for pyruvate {ECO:0000269|PubMed:9038349};
CC KM=88 uM for ATP {ECO:0000269|PubMed:9038349};
CC KM=341 uM for phosphate {ECO:0000269|PubMed:9038349};
CC Temperature dependence:
CC No loss of activity below 10 degrees Celsius.
CC {ECO:0000269|PubMed:9038349};
CC -!- PATHWAY: Photosynthesis; C4 acid pathway.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
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 -!- DOMAIN: The C-terminal domain (831-955) is involved in cold-tolerance.
CC -!- PTM: Phosphorylation of Thr-535 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: A short cytoplasmic isoform may be produced by
CC alternative promoter usage. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family. {ECO:0000305}.
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DR EMBL; X79192; CAA55784.1; -; Genomic_DNA.
DR EMBL; U08399; AAA86940.1; -; mRNA.
DR PIR; S56649; S56649.
DR AlphaFoldDB; Q39734; -.
DR SMR; Q39734; -.
DR PRIDE; Q39734; -.
DR BRENDA; 2.7.9.1; 2265.
DR SABIO-RK; Q39734; -.
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 ATP-binding; Chloroplast; Direct protein sequencing; Kinase; Magnesium;
KW Metal-binding; Nucleotide-binding; Phosphoprotein; Photosynthesis; Plastid;
KW Transferase; Transit peptide.
FT TRANSIT 1..71
FT /note="Chloroplast"
FT /evidence="ECO:0000269|PubMed:7766886"
FT CHAIN 72..955
FT /note="Pyruvate, phosphate dikinase, chloroplastic"
FT /id="PRO_0000023560"
FT ACT_SITE 537
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 915
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 643
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 700
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 829
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 829
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="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 852
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 853
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 853
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 535
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250"
FT CONFLICT 10
FT /note="P -> L (in Ref. 1; CAA55784)"
FT /evidence="ECO:0000305"
FT CONFLICT 28
FT /note="T -> I (in Ref. 1; CAA55784)"
FT /evidence="ECO:0000305"
FT CONFLICT 205
FT /note="A -> G (in Ref. 1; CAA55784)"
FT /evidence="ECO:0000305"
FT CONFLICT 263
FT /note="A -> V (in Ref. 1; CAA55784)"
FT /evidence="ECO:0000305"
FT CONFLICT 684
FT /note="D -> S (in Ref. 1; CAA55784)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 955 AA; 104225 MW; 359BCD0FA950E890 CRC64;
MSSLFVEGMP LKSANESCLP ASVKQRRTGD LRRLNHHRQP AFVRGICRRK LSGVSRIELR
TGGLTLPRAV LNPVSPPVTT TKKRVFTFGK GNSEGNKDMK SLLGGKGANL AEMASIGLSV
PPGLTISTEA CEEYQQNGKK LPPGLWDEIL EGLQYVQKEM SASLGDPSKA LLLSVRSGAA
ISMPGMMDTV LNLGLNDEVV DGLAAKSGAR FAYDSYRRFL DMFGNVVMGI PHSLFDEKLE
QMKAEKGIHL DTDLTAADLK DLAEQYKNVY VEAKGEKFPT DPKKQLELAV NAVFDSWDSP
RANKYRSINQ ITGLKGTAVN IQCMVFGNMG NTSGTGVLFT RNPSTGEKKL YGEFLVNAQG
EDVVAGIRTP EDLVTMETCM PEAYRELVEN CVILERHYKD MMDIEFTVQE NRLWMLQCRT
GKRTGKGAVR IAVDMVNEGL IDTRTAIKRV ETQHLDQLLH PQFENPSAYK SHVVATGLPA
SPGAAVGQVV FSAEDAETWH AQGKSAILVR TETSPEDVGG MHAAAGILTA RGGMTSHAAV
VARGWGKCCV SGCADIRVND DMKVFTIGDR VIKEGDWLSL NGSTGEVILG KQLLAPPAMS
NDLETFMSWA DQARRLKVMA NADTPNDALT ARNNGAQGIG LCRTEHMFFA SDERIKAVRK
MIMAVTPEQR KAALDLLLPY QRSDFEGIFR AMDGLPVTIR LLDPPLHEFL PEGDLEHIVN
ELTADTGMSK DEIYSRIEKL SEVNPMLGFR GCRLGISYPE LTEMQVRAIF QAAVSMNNQG
VTVIPEIMVP LVGTPQELRH QIGVIRGVAA NVFAEMGLTL EYKVGTMIEI PRAALIADEI
AKEAEFFSFG TNDLTQMTFG YSRDDVGKFL PIYLSQGILQ HDPFEVLDQK GVGQLIKMAT
EKGRAANPNL KVGICGEHGG EPSSVAFFDG VGLDYVSCSP FRVPIARLAA AQVVV
